The Phoney War: September 1939 - March 1940

References
Appendix IV Organisation of RN S/Ms at the outbreak of War (3 Sept 1939)
Appendix V Submarine re-organisation November 1939
Patrolgram 1 Patrols at Home
Patrolgram 2 Patrols abroad during Phoney War
Map 1 Disposition of RN S/Ms at beginning of War
Map 2 Disposition of RN S/Ms late Oct - early Nov 3
Map 3 Disposition of RN S/Ms end Nov 39 (intercept of Scharnhorst)
Map 4 Incidents and contacts during Phoney War

THE OUTBREAK OF THE SECOND WORLD WAR, when it came, was certainly not unexpected. The succession of events since Hitler came to power in 1933: the re-occupation of the Rhineland; the Anschluss with Austria; Munich and the invasion of Czechoslovakia each made war more likely. Finally the British guarantee to Poland given early in 1939 made war practically certain. Although the formal warning telegram was not sent out until Germany actually invaded Poland on 1st September, active preparations had been in progress for more than a month. Summer leave in the Home Fleet was given early in July before war preparations were taken and then the preparations were cloaked as exercises. Submarines in reserve began to be manned as early as 3rd July.

Since the mobilisation of the previous autumn, some changes had been made in the submarine war plans. Clearly the issue of sealed patrol orders direct to submarines from the Admiralty was unsatisfactory. It had now been decided that when RA(S) took command of the two operational flotillas in the North Sea, he would issue their orders. The base of the Second Submarine Flotilla had had to be moved from Aberdeen to Dundee because of the size of the new depot ship Forth. The minelaying in the estuaries of the German rivers was reconsidered as it had to be done in very shallow water and was scarcely practicable. In the end it was cancelled and the minelaying submarines were earmarked to reinforce the Mediterranean where the C-in-C had a plan to use them.

By the middle of August, all the submarines in reserve had been fully manned and all submarines in commission had been stored and were ready for war. By 26th August the depot ships Forth and Titania had arrived at their war stations at Dundee and Blyth respectively and the submarines of their flotillas had joined them. The Fifth Flotilla took over all other submarines in home waters including those building and refitting¹. RA(S) set up his operational headquarters at Aberdour on 30th August.

At the outbreak of war, the Admiralty considered that Scharnhorst and Gneisenau and the pocket battleships were the greatest danger to our trade routes. The U-boats were not expected to compete with asdic and Germany, for what it was worth, had anyway agreed in the Anglo-German Naval Agreement only to operate them against merchant shipping in accordance with International Law. Reconnaissance in the North Sea to detect enemy warship raiders putting to sea was therefore considered to be of the greatest importance. This was especially so as we had made no progress in breaking the German ciphers in the way we had done in the First World War. It had therefore already been decided, well before the outbreak of war, to start air reconnaissance of the North Sea by RAF Coastal Command. This consisted of a patrol across from Montrose in Scotland to Obrestadt in Norway, but the Anson aircraft allocated to this duty had insufficient range to reach the coast of Norway. RA(S) was therefore ordered to fill the gap with a patrol line of five submarines twelve miles apart. This task was given to the Second Flotilla and the Obrestadt line, as it was called, was in place over a week before war began². On 31st August all six boats of the Sixth Flotilla from Blyth sailed to take up positions in the Heligoland Bight on an arc from Horns Reef to Terschelling³. These dispositions were intended to intercept any German warships or U-boats leaving for the Atlantic as commerce raiders before the outbreak of war. (See Map 1). In this our patrols failed because they were too late. Fourteen U-boats left Germany for areas west of the British Isles on 19th August followed by two more on 22nd-23rd; the pocket battleship Graf Spee left for the South Atlantic on 21st August and her sister Deutschland for the North Atlantic on 24th August. Their supply tankers Altmark and Westerwald also sailed during the same period.

British submarine movements before the outbreak of war included the departure on 25th and 27th August of five submarines to reinforce the Mediterranean⁴. The two fleet submarines Severn and Clyde had already left Malta for their war station at Gibraltar⁵. The Mediterranean Fleet had already left with the depot ship Maidstone for Alexandria leaving the remaining submarines of the First Flotilla at Malta where they were joined by the reinforcements from home. On 30th August the Admiralty told the C-in-C Mediterranean that any defensive precautions against Italy were not to be provocative. The submarines, therefore, were not sent out on patrol but were simply kept ready at Malta. This was acceptable as reconnaissance against the Italian Fleet was of less importance than against the Germans as we had been decrypting the Italian ciphers since 1937 and our intelligence of their movements was good. Next day the British Ambassador in Rome was informed by the Italian Government that Italy did not intend to go to war with Britain or France and this statement was supported by what we had learnt from signal intelligence.

On the Obrestadt line, relief submarines continued to be sent out from Dundee, the latest being Oxley and the brand new Triton. These two took their places on the patrol line but on the night of 10th September were both seriously out of position. They sighted each other and Triton (Lieutenant Commander HP de C Steel RN) made the challenge by signal lamp. She got a garbled and unsatisfactory reply and, thinking Oxley must be a U-boat, fired three torpedoes one of which hit and sank her¹¹. This disaster, the first loss of one of our submarines in the Second World War, should, of course, never have happened. Two survivors, one of which was Lieutenant Commander HG Bowerman RN, Oxley's Captain, who was on the bridge at the time, were picked up by Triton, but four officers and fifty-five men were either killed by the explosion of the torpedo or drowned when Oxley went down. The material loss of this elderly and not very reliable boat was not serious but we could ill afford to lose her trained and experienced crew. Oxley had been thrown into the fray straight from reserve with no time to work up, but it is doubtful if this fact contributed to her loss. This accident was kept secret so there was no public outcry but it could not be concealed from the home submarine command. It illustrated the difficulties in war and its lessons were learnt albeit by the hard way. The distance apart of submarines on the patrol line was then increased to sixteen miles not only for safety's sake but to close the gap left by the loss of Oxley. Three days later and before the loss of Oxley was generally known, Sturgeon (Lieutenant GDA Gregory RN) outward bound from Dundee met Swordfish (Lieutenant CB Crouch RN) returning from patrol in the early morning light. She fired three torpedoes but Swordfish had sighted her and dived, two of the torpedoes passing over the top of her. This second near disaster was attributed to bad staff work as neither Sturgeon nor Swordfish had been informed of the other's presence. The next submarine to leave Dundee, Seahorse, was again attacked but fortunately unsuccessfully by an aircraft of Coastal Command. On 17th September, when still on passage and 110 miles east of Dundee she came upon U36 attacking a Danish merchant vessel with her gun. Seahorse (Lieutenant DS Massy-Dawson RN) fired two torpedoes at long range but they missed¹². On arrival on the Obrestadt line, Seahorse was ordered to close the coast off Lister and Triton off Skudenes to try and intercept some German iron-ore ships reported by our consuls to be off Haugesund. They failed to find them but they stopped and investigated several neutral merchant ships before returning to their stations.

By now, submarine operations had settled down to a routine. At the outbreak of war it was by no means clear how they were to be operated. We have seen how the whole Sixth Flotilla was sent out from Blyth together to patrol in the Heligoland Bight and how, when their time was up, they all had to return simultaneously without any boats being available to relieve them. In the Second Flotilla, however, as the requirement was for only five boats for the Obrestadt line, it was possible to provide reliefs so that the patrol line could be kept in place continuously. The staff of the C-in-C seemed at first to favour submarines being operated like its ships. That is to put to sea en masse to carry out specific operations and then return to base, refuel as quickly as possible and remain available in harbour at short notice until required again. The depot ships disliked submarines being kept at short notice as this made any serious repairs or maintenance impossible. Furthermore the submarine crews could not be sent on leave or even have reasonable rest periods. Operationally in any case, submarines with their slow speed could seldom be sent out in emergency in time to be of any use. It was clear that if they were to be of any use for reconnaissance or attrition should the enemy put to sea, some of them must be on patrol all the time. The solution, long known to the submarine world, was to use a cycle of war patrols in which roughly half the submarines were always at sea and half in harbour resting and maintaining at reasonable notice. The length of time submarines were kept at sea varied with their size and the theatre of operations. In the North Sea it was normally ten to fourteen days whilst in the South Atlantic, Far East and Indian Ocean it was more like a month.

AT THIS POINT IT IS APPROPRIATE to describe in more detail a 'submarine war patrol'. We begin with the submarine at its base alongside her depot ship. Here, 'being in all respects ready for sea' as the sailing orders put it, the submarine would sail with all defects remedied, all maintenance routines and tests done and fully stored, fuelled and complete with torpedoes and ammunition. The Commanding Officer would have been given his orders in which he would be told the object of his patrol; the area to be occupied and for how long as well as the route to be taken to and from the area and any restrictions or special instructions that might be necessary. The submarine would find a small warship waiting to escort her clear of the harbour and well out to sea where she would be unlikely to meet so-called 'friendly' ships or aircraft. The function of this escort was to protect the submarine not from her enemies but from her friends, both ships and aircraft. The escort's presence, leading the submarine to sea, was intended to ensure that all concerned would realise that it was not an enemy U-boat. On parting from the escort the submarine would probably make a practice dive to 'catch a trim' and ensure that everything was in full working order. She would then set off by herself on the surface following the route ordered and zigzagging if her Captain deemed there to be a danger from prowling U-boats. Her lookouts would be closed up with one third of her crew on watch below, and she would be in instant readiness to dive if ships or aircraft were to be sighted. 'Friendly' aircraft would have been given a 'bombing restriction area', which was a rectangle several miles long and wide, which moved at the speed of the submarine. The submarine had to keep in this area and friendly aircraft should keep out of it. In this fashion the submarine, proceeding on its diesel engines on the surface at about 12 knots¹³ would cross the North Sea both by day and night.

On the dispersion of the Obrestadt line, our submarines were sent to patrol off the south-west coast of Norway, off the Skaw and in the Skagerrak as well as on both sides of the German declared mined area. At this time there were no submarines on patrol in the Heligoland Bight itself. Also at this time an important change was made in the role of submarines on patrol. The object was altered to allow them always to attack first and make a reconnaissance report afterwards if necessary. The old policy of not attacking if it jeopardised making a report had validity in the days of the Grand and High Seas Fleets when knowledge that the enemy was at sea was of paramount importance. However it made little sense when a pocket battleship was breaking out into the Atlantic when a single torpedo hit could force her to return to base.

On 24th September, Spearfish (Lieutenant JH Eaden RN) patrolling north of Hanstholm in Denmark, was detected by a force of German anti-submarine trawlers, which were now fitted with hydrophones and a primitive echo detection set. They also had depth charges and guns¹⁶. Spearfish was hunted all day and suffered a number of depth charge attacks, which damaged her badly. It seems likely that the German anti-submarine vessels were stopped or patrolling slowly during the night listening on their hydrophones. They probably picked up Spearfish while she was still on the surface using her diesel engines and closed in picking her up again after she dived. Spearfish was not using her asdic to listen as her dome was raised because of the shallow water. At 0715 when the Germans dropped a depth charge close ahead, Spearfish bottomed in 84 feet, stopping all machinery. At 0900 she decided to come to periscope depth to see what was going on. As soon as she started her ballast pump, however, a depth charge was dropped close and she remained on the bottom. At 1720 the Germans made contact with some kind of sweep or towed charge. A very close explosion put lights out and caused serious structural damage as well as jamming the after hydroplanes. The enemy then seems to have lost contact and, after dark at 2045, Spearfish was able to struggle to the surface. It was a clear, dark night and there was nothing in sight. She got both diesel engines going after two hours and crawled away. She decided not to signal for help at once for fear that the transmissions would be picked up by enemy direction finding stations. She made a signal before daylight, however, and Coastal Command aircraft and ships of the Home Fleet were despatched to her assistance. Rendezvous was made at 0400 on 26th September with ships of the Second Cruiser Squadron and she was escorted to Rosyth where she arrived on 27th. Spearfish was out of action under repair at Newcastle for nearly six months. Just over a week later on the night of 5/6th October in the same area, Seawolf (Lieutenant Commander JW Studholme RN) in bright moonlight sighted a Nurnberg-class cruiser. The range was long and as she was about to fire the target turned sharply away. As a forlorn hope Seawolf fired two torpedoes after her but it is doubtful if they even reached her track¹⁷.

Towards the middle of September, another elderly submarine joined the Second Flotilla from reserve. This was Oberon, which had been in Portsmouth dockyard since the outbreak of war having a number of defects remedied. On arrival at Dundee she had to have more defects taken in hand by the depot ship Forth but was got away on patrol on 22nd. She was sent to patrol to the northwest of the German declared area and sighted some aircraft, some fishing vessels and a few merchant ships. She had more trouble with one of her main motors and then her after hydroplanes broke down and she had to surface in daylight. In addition her asdic set type 116, was inefficient. On return to Dundee she was declared to be unfit for operations and was sent back to Portsmouth and relegated to training duties.

A week earlier the elderly H34 missed a U-boat off Kinnaird Head. H34 (Lieutenant Commander BT Simons RN) was on passage to Scapa Flow in company with the trawler Euryalus. A German U-boat, probably U13 approached Euryalus to investigate her and two torpedoes were fired by H34 but missed. H34 and Euryalus continued to Scapa Flow from where they operated in company west of the Orkneys throughout October without success. This was the first use of submarines deliberately against U-boats during the Second World War. Other contacts with U-boats by our submarines had all been by chance when they were on patrol in the North Sea¹⁸.

In October, the German Navy made its first sortie with one of its main units. Gneisenau, Koln and nine destroyers sailed under Admiral Boehm on 7th October and were sighted by Coastal Command off the Lister Light just after midday on 8th October. Their purpose was to entice units of the Home Fleet over a concentration of four U-boats and within range of the Luftwaffe, which had recently allocated a number of bomber squadrons for naval cooperation. Coastal Command shadowed the force to a position thirty miles west of Stattlandet. The Home Fleet took up positions to intercept assuming that a break out into the Atlantic was taking place, but after dark the German squadron reversed course and returned to Kiel. They passed the Skaw at about midnight on 9th October¹⁹. There were no less than nine British submarines on patrol or on passage in the North Sea during this sortie, but nothing was seen. Starfish and Sterlet were off the west coast of Norway; Thistle was off the south coast and Sturgeon was relieving Seawolf in the Skagerrak. Triton was also on her way to the Skagerrak, while Triumph was on her way back to Dundee and L26 and H32 were in the Dogger Bank area. Visibility was good and the German ships were off Norway for two days in daylight. This was disappointing but serves to show, if nothing else, that the sea is a very large place.

Although no ship was hit, air attacks on the Humber Force on 9th October had shown that the Luftwaffe was prepared to deploy a considerable number of bombers in support of naval operations. It was, of course, realised that our east coast naval bases were also well within range of them. Especially vulnerable were the submarine bases at Blyth and Dundee, which had virtually no anti-aircraft defences. On 13th October, therefore, the Admiralty ordered the Second and Sixth Submarine Flotillas to move to Rosyth where air defences, although not particularly strong, were at least in existence²⁰. This was not a moment too soon and on 16th October the Luftwaffe attacked. However they targeted ships in the Firth of Forth and next day in Scapa Flow as well. In the raid on Rosyth, Forth came into action with her powerful anti-aircraft armament and claimed to have shot down an enemy aircraft.

Finally, some other Cs-in-C abroad were asking for submarines. C-in-C North Atlantic wanted them to watch the ports in the Iberian peninsular where German merchant ships had taken refuge. This need, however, was met by the French submarines Achille, Casabianca, Pasteur and Sfax patrolling in turn off Cape Ortegal. C-in-C East Indies asked for four submarines from the China Station as he had few ships of heavy enough metal to fight a pocket battleship, should one round the Cape into the Indian Ocean.

Since the outbreak of war only one British submarine had been lost, while six submarines had just returned from the Mediterranean and two Polish submarines had escaped from the Baltic and had joined the Home Fleet²⁵. These reinforcements had to be fitted into the organisation. The Admiralty finally approved the disposition shown in Appendix IV, which is dated 5th November. By this the Second Flotilla was to be composed of T-class submarines with the two Poles and the minelayers from the Mediterranean and was to be used for anti U-boat patrols north and west of the British Isles. A new Third Flotilla composed of S-class submarines was to be formed at Harwich using the old depot ship Cyclops that had just completed a refit at Malta²⁶. This Third Flotilla and the Sixth Flotilla (which was shortly to move back to a shore base at Blyth and had been reinforced by some S-class submarines)²⁷ were to operate in the North Sea against German surface ships and U-boats as before. Abroad the two River-class were to continue their anti-raider patrols in the central Atlantic where Graf Spee and Deutschland were known to be operating. They were to have the depot ship Maidstone from Alexandria to support them. Four O-class were to be moved from the Far East to Colombo where, as the Eighth Flotilla with the old depot ship Lucia ²⁸ they were to operate against raiders in the Indian Ocean.

The ink was scarcely dry on some of these decisions before the Admiralty changed its mind. The Second Flotilla was to continue operations in the North Sea and the three minelayers were to cross the Atlantic to operate as part of the Halifax escort force to protect convoys from attack by raiders. The three minelayers sailed from the United Kingdom in mid November. The decision to use the Second Flotilla in the North Sea instead of on anti U-boat patrols in the Atlantic was taken by the Admiralty because of the First Lord's desire to do something about the Swedish iron ore trade to Germany. This was also probably the flotilla earmarked to enter the Baltic as part of 'Plan Catherine'. The Admiralty also hoped to use the new Third Flotilla to try and stop coastal traffic from Belgium and Holland to Germany.

IN THE EARLY PART of November, five submarines were kept on patrol off the coast of Norway, in the Skagerrak and on both sides of the German declared area. There were no important contacts but much useful information was amassed about the routes of enemy and neutral merchant ships. Sealion (Lieutenant Commander B Bryant RN) on patrol west of the German declared area, found an enemy secret passage through it marked by a buoy. On 14th November, the pocket battleship Deutschland, which had engine trouble in the North Atlantic, broke back through the Skagerrak to Germany. There were seven submarines on patrol at the time but she avoided being seen by any of them^29. She used bad weather and the long nights skilfully and evaded the ships of the northern patrol and the air reconnaissance flown by Coastal Command aircraft with the same ease.

On 20th November, Sturgeon (Lieutenant GDA Gregory RN) was working her way southwards behind the German declared area. Here she encountered some enemy anti-submarine trawlers. Our submarines had deduced from contacts with these vessels that their hydrophones worked much better when they were stopped. Sturgeon decided to discourage them from such tactics and, closing stealthily to 1000 yards, fired four torpedoes at two of these stopped trawlers. Sturgeon lost trim on firing and did not see the result. One torpedo, however, hit and sank V209 (the trawler Gauleiter Telshow). This was, in fact, the first successful torpedo attack by a British submarine in the Second World War. Altogether there had been eight previous torpedo attacks on the enemy in which 24 torpedoes had been fired and there had not been a single hit. Of these attacks, the enemy avoided one, two were 'forlorn hopes' anyway, in three too few torpedoes were fired and in the remaining two the failure can only be put down to some other unknown cause including bad luck.

In the early afternoon of 21st November, the German battle cruisers Scharnhorst and Gneisenau escorted by Koln, Leipzig and three destroyers, left Wilhelmshaven and proceeded north at high speed between the German declared area and the Danish coast. They passed Sturgeon off Horns Reef and L23 off Little Fisher Bank during the night without being seen. Their escort was then detached to the Skagerrak. The two battle cruisers then avoided Coastal Command reconnaissance and passed north of the Shetlands and Faeroes into the Iceland - Faeroes gap³⁰. Here on 23rd November Scharnhorst destroyed the armed merchant cruiser Rawalpindi of the Northern Patrol and this was the first indication to the British that the two ships were at large. Energetic measures were at once taken to intercept the two ships during their return to Germany. Triumph, Triton and Trident were sailed from Rosyth, Starfish and Undine from Blyth, Sunfish and Snapper from Harwich and the brand new Truant from the Channel. Starfish was sent to reinforce Sturgeon east of the German declared area and Snapper to the west of it while the rest were to form a patrol line south west of the Lister Light to cover both the entrance to the Skagerrak and the Horns Reef passage³¹.

Throughout December, submarines continued their patrols off the south and west coasts of Norway, in the Skagerrak and off the Skaw and were able to bring back valuable intelligence of the number and routes of both German and neutral shipping in these areas. Most of the shipping, however, was immune from our contraband control as it was in neutral waters. Submarines from Harwich patrolled off the Dutch coast in the same way. Snapper was sent on this duty towards the end of December. When trying to get close enough to intercept ships at night she ran ashore again. This time she was in low buoyancy and was able to blow main ballast and refloat herself without difficulty. She was later forced to dive at night by enemy patrols and was hunted. On 26th December Triumph on passage across the top of the German declared area struck a mine right forward. Striking a mine normally means the total loss of a submarine but in this case she survived³⁶. She reported her predicament and after sighting an enemy flying boat, was escorted back to Rosyth by Coastal Command and the Home Fleet and arrived there on 28th December. Triumph was under repair in Chatham dockyard for nine months.

Soviet Russia had invaded Finland at the end of November and the League of Nations had asked its members to give what help they could to the Finns. The freezing of the Baltic meant that no help could be sent that way until the spring. On 28th December Trident left Rosyth for North Russia to patrol off Murmansk. Here she might be able to help if Russia made a seaborne attack on Petsamo on the Arctic coast of Finland and there were rumours that Russia might extend her aggression to north Norway. There were also still a number of German merchant vessels in Murmansk and it was known that U38 had visited the area. Trident returned in mid January without having seen anything but with the assurance that patrol in these waters could be undertaken by our submarines even in mid winter if necessary.

In the South Atlantic, Severn and Clyde continued their patrols, supported from late November by Maidstone at Freetown. Clyde made a number of patrols in the vicinity of the Cape Verde islands and Severn crossed the Atlantic to work near St Paul's Rocks off the Brazilian coast. Graf Spee was at this time commerce raiding in the South Atlantic but still never came within a thousand miles of either submarine. In mid November, Graf Spee rounded the Cape and on 15th captured a ship in the Mozambique Channel thus revealing her position. At this time Olympus from the Eighth Submarine Flotilla at Colombo was in the Seychelles area and Otus and Odin were in the vicinity of the Chagos and Maldive Islands. Olympus was at once ordered to the Mozambique Channel. On the other side of the Indian Ocean, one submarine was sent from Singapore to patrol in the islands west of Sumatra and two submarines were sent to patrol the Lombok Strait³⁷. It was also considered possible that GrafSpee might make for Vladivostok where, after the Soviet-German Pact, Russia was believed to be ready to accommodate her. There were also fears that German U-boats might operate from that port and, with Russia's attack on Finland, she was considered hostile by the Allies in any case. Our submarine patrols off Japan were therefore discontinued and Regulus in mid December was sent to patrol off Vladivostok. Here she sighted a Soviet submarine and watched a Soviet anti-submarine exercise as well as reconnoitring a number of anchorages for German merchant ships.

In December, Severn, who had meanwhile returned to Dakar, was sent south to protect the whaling fleet in South Georgia. She was still 500 miles north of Trinidad when the battle of the River Plate took place on 13th December. She was at once ordered to Montevideo to blockade the Graf Spee there but long before she could get there, Graf Spee destroyed herself and Severn was ordered back to Freetown. The French now offered to send four submarines to the South Atlantic and Maidstone, Severn and Clyde were ordered home. In mid December, radio intelligence indicated that a raider was probably at Prince Edward or Crozet Islands in Antarctica, over 1000 miles south-east of the Cape. Olympus, then to the north of Durban, was sent to investigate. She found nothing but suffered appalling weather both stormy and very cold. She returned to Durban by the end of the year.

On 8th January 1940, Vice Admiral Sir Max Horton KCB DSO* relieved Rear Admiral BC Watson CB DSO and hoisted his flag as Vice Admiral (Submarines)(VA(S)). Admiral Horton, a submarine 'ace' of the First World War, was famous for his exploits in E9 in the Baltic in 1915. He had not, however, held a submarine appointment for ten years and was somewhat senior for the post, which was normally held by a Rear Admiral. He had come from command of the Northern Patrol, an appointment he had held since the outbreak of war. Rear Admiral Watson was promoted to Vice Admiral and retired, although he was later appointed to be Flag Officer in charge at Greenock. During the winter there were a number of changes among senior officers in the submarine command. The Chief Staff Officer, Captain IAP MacIntyre RN had completed his time and his relief, Captain GCP Menzies RN had been nominated before the war began. Captain Menzies actually arrived to take up his appointment and as a graduate of the RN Staff College was eminently suitable for the job. Nevertheless it was decided that a change was undesirable and Captain MacIntyre was required to stay at his desk at Fort Blockhouse. Captain Menzies accompanied Admiral Watson to Aberdour and became Chief Staff Officer (Operations). With the arrival of Admiral Horton, Captain Menzies was sent to command the Second Submarine Flotilla in place of Captain WD Stephens RN and took up his post in March³⁸. Captain MacIntrye remained as Chief Staff Officer with responsibilities for Administration and Personnel until the end of 1941. Captain ER Gibson RN took over as Chief Staff Officer (Operations) relieving Captain Menzies. The Third Submarine Flotilla formed at Harwich in November 1939 was commanded by Captain P Ruck-Keene RN from the First Flotilla in the Mediterranean who had returned with most of his flotilla. The three submarines left at Malta were commanded by Commander GP Claridge RN as Senior Officer (Submarines) in the Mediterranean. Commander Bethell was also due for relief in 1940 and Captain GAW Voelcker RN took over the command of the Sixth Submarine Flotilla in May. The Eighth Flotilla formed at Colombo with the depot ship Lucia was commanded by Commander SM Raw RN sent out for the purpose.

One of the early changes made by Admiral Horton concerned the appointment of submarine Commanding Officers. There were seven Commanders in command and about eighteen Lieutenant Commanders on their third or fourth commands who were mostly over the age of thirty-five. From his experience of the First World War, Admiral Horton considered this to be too old. He therefore set about relieving these officers with younger men obtained by 'clawing back' the qualified submarine captains who had been sent to general service after their first commands. There were some twenty-five of these officers serving in the fleet. Some of the older officers were required for command and staff appointments to do with submarines but the surplus returned to general service. There is little doubt, however, that age was not Admiral Horton's only concern. All the submarine successes so far achieved in the North Sea had been by the younger submarine captains and it seems that he doubted the offensive spirit of some of the inter war trained Commanding Officers. A number of these officers had, in fact, already asked to return to general service. No doubt this attitude can be attributed to a certain extent to the atmosphere engendered by the Admiralty policy for the abolition of the submarine, by the paramount importance of safety in peacetime exercises, and by knowledge of the effectiveness of modern anti-submarine measures such as asdic. Admiral Horton's 'purge' as it became known, was not governed entirely by age and he made some notable exceptions and also kept many of these older officers in command and staff appointments. Nevertheless some twenty older officers were relieved in command by younger officers. Another decision made by Admiral Horton at this time was to use officers of the Royal Naval Volunteer Reserve in submarines and the first two were selected during the summer. He also approved the drafting of &'hostilities only' ratings for the crews of submarines.

During February, efforts continued to try and capture German ships carrying iron ore and although a number of neutral ships were boarded, none was sent in and no German ships were encountered. Sealion intercepted two merchant ships, but one claimed to be Latvian and the other a Finn. It was too rough to send a boarding party and she had to let both ships go. The German tanker Altmark, which had acted as a supply ship for Graf Spee in the South Atlantic and had prisoners on board, succeeded in evading our surface and air patrols and reached the coast of Norway on 14th February. Our Consul at Bergen reported her as she passed south and was intercepted and boarded by the destroyer Cossack in Josing Fjord on 16th, the prisoners being rescued. The destroyers then withdrew but the submarines Seal, Orzel and Triad were also directed to Josing Fjord. Next day Seal, and Orzel were ordered to resume their normal patrols but Triad was left with orders to torpedo Altmark if she left Norwegian territorial water. Altmark was clearly not a bona fide merchant ship and being a naval auxiliary, could be torpedoed without warning under international law.

Submarine escorts for the Norwegian convoys continued in the New Year, Triton, L23, Orzel, Thistle, Seal and Narwhal all doing this duty. Most escorting trips were uneventful but on 18th February, Thistle with HNI2 saw the destroyer Daring sunk by a U-boat and was able to draw the attention of other ships of the escort, who had not seen anything, so that some survivors were rescued. Shortly afterwards, on 25th February, Narwhal with HN14 sighted a U-boat astern of the convoy and informed destroyers of the escort who were able to sink U63.

Scharnhorst and Gneisenau were ready for another sortie by 18th February⁴⁰ They left Wangeroog in the East Frisian Islands with the cruiser Hipper and nine destroyers on what was known by them as Operation 'Nordmark'. Its aim was to destroy the Norwegian convoy, which had already left the Firth of Forth for Bergen⁴¹. All except two of the destroyers were detached to operate in the Skagerrak. At the time there were no British submarines on patrol in the Heligoland Bight and the German ships sped northwards through the night. They had, however, been sighted by chance as they were leaving harbour by Bomber Command aircraft on a leaflet raid and were reported. The aircraft, however, said that the ships appeared to be stuck in the ice near Heligoland and that the sea was frozen for ten miles west of the island. The Home Fleet was in the Clyde but at once put to sea although it was doubtful whether they could arrive in the North Sea in time to protect the convoy, which was consequently ordered in to Scapa Flow. This precaution was clearly necessary but it deprived Narwhal, of the escort, the opportunity to show what a submarine could do to protect a convoy against an attack by surface ships. There were, however, five submarines on patrol off Norway, in the Skagerrak and in the central North Sea and two more to the west of the German declared area. These were at once re-disposed to meet the situation. VA(S) decided that this was the time for submarines to return to the Heligoland Bight. Salmon was ordered to a position near Heligoland itself, proceeding south of the German declared area while Sunfish was told to cross the declared area by the passage found by Sealion and to patrol at its eastern end. Orzel was ordered to Horns Reef and L23 and Seal were positioned to the north of the declared area. Triton was ordered to join Triad off Josing Fjord in case the object of the German ships was to rescue Altmark. Finally Truant left Rosyth to fill the gap between Triton and Seal. These dispositions were not completed in time to catch the enemy on his way north although most of the submarines involved were in the right general area. However nothing was seen by any of them.

On 6th March, Unity (Lieutenant JFB Brown RN) on patrol off Josing Fjord sighted Altmark steering down the coast in territorial waters escorted by Norwegian destroyers. Unity gave chase on the surface outside the three-mile limit and reported by wireless. Coastal Command sent out reconnaissance aircraft and when Unity lost touch, she was ordered, with Orzel, to try and intercept off Hanstholm. Altmark, however, was not seen again and she escaped back to Germany. Ursula, in the middle of the month, met ice in the Kattegat and damaged one of her periscopes and her bow torpedo tube shutters. After dark on 21st March she encountered the German merchant ship Heddernheim of 4947 tons carrying 7000 tons of iron ore. The order to stop had to be enforced not only by a shot across the bows but another over the funnel. The ship was abandoned and then sunk by torpedo⁴⁴. Ursula (Commander GC Phillips DSO RN) left the crew in the ship's boat but took the Chief Engineer prisoner. They were close to land and there were other ships in the vicinity to pick them up. Two days later (23rd March), Truant (Lieutenant Commander CH Hutchinson RN) came upon the German Edmund Hugo Stinnes of 2189 tons off Bovberg Light. She was stopped and she scuttled herself. As she was making a distress signal, Truant fired a number of live rounds at the bridge. After taking the Master prisoner from the boats, her sinking was expedited by torpedo⁴⁵. The ship was found to be carrying coke to Copenhagen. VA(S) noted that in both these sinkings, the submarine's instructions had been slightly exceeded but that he did not intend to do anything about it as providing such sinkings were outside territorial waters and the crews were saved, international repercussions were unlikely.

At the end of March, the first of the German Armed Merchant Raiders, Atlantis, broke out into the Atlantic. She left the Baltic disguised as a Russian merchant ship and proceeded up the coast in neutral waters until, when far to the north she turned west passing north of Iceland and out through the Denmark Strait. Our submarines therefore could only have intercepted her if she had left territorial waters and even then they would have to have visited and searched her and this would have been a very dangerous move. There were few other incidents in March: the rescue by Unity of some Dutch fishermen whose vessel had been attacked by the Luftwaffe was one and the stalking of an anti-submarine trawler by Sealion (Lieutenant Commander B Bryant RN) east of the declared area was another. Her presence was suspected and the hunter became the hunted fortunately without serious consequences.

In the Far East, Japan was causing us no anxiety and was busy with her war in China. The submarines at Hong Kong were used to continue patrols off Vladivostok. Rainbow and Proteus followed Regulus and each made a patrol but sighted nothing of interest. The weather conditions were, however, appalling. In the Indian Ocean, Odin and Olympus were used to search the Chagos and Maldive Islands before the passage of the ANZAC troop convoy to the Middle East and to see it safely through the Nine Degree Channel.

At the end of March, VA(S) moved his headquarters from Aberdour to a block of flats at Northways, Swiss Cottage in London. Here he was able to re-unite his operational and administrative staff and he was in much closer contact with the Admiralty and with the Air Officer C-in-C, Coastal Command. Although operationally he was still under the command of the C-in-C, Home Fleet, this meant very little. C-in-C was often at sea in his flagship and even when in harbour was at one of a number of places and difficult to contact. In any case VA(S) had to deal with submarines operating in the areas of other Cs-in-C as well as with the overall strategic oversight of all submarines. Of equal importance was the expansion of the submarine branch involving the building of new submarines, deciding their characteristics and arranging for their maintenance and the recruitment and training of their crews. It was with the Admiralty that he had to be in contact for these matters.

Since the outbreak of war, four submarines had been lost in operations and⁴⁶ two had been badly damaged and were still under repair⁴⁷. Five submarines⁴⁸ originally considered fit for operations had been or were about to be downgraded to training duties. Against these reductions in strength, four new T-class submarines had become operational⁴⁹, nine submarines had joined VA(S) flag from abroad⁵⁰ and two Polish submarines⁵¹ were now in service alongside the Royal Navy. So there were now six more submarines operational in home waters than there were at the outbreak of war. In addition, seven more T-class of pre-war programmes were due to complete during 1940 and Thetis, lost on trials just before the war, had been salved, renamed Thunderbolt and would also come into service in the autumn. Immediately after the outbreak of war, seven more T-class and twelve U-class had at once been ordered. In addition, five of an enlarged S-class were ordered in January and ten more U-class in early March. This made a grand total of forty-four submarines in various stages of construction.

At the end of March, the seven month long 'Phoney War' came to an end. So called because of the total lack of activity on land in the west and the leaflet raids over Germany, the Phoney War was anything but phoney at sea. Our submarines were very busy and carried out 211 patrols, mostly in the North Sea but also in the oceans from the Arctic to the Antarctic, and from Halifax to the Lombok Strait. Admittedly in their principal aim of intercepting and reporting surface ships sortying from their bases, they did not do very well. They failed to sight any of the three operations by the German battle cruisers as they put to sea and saw nothing of the return of the raider Deutschland. They did intercept the ships of operation 'Nordmark' as they returned but were unable to attack. The torpedoing of two light cruisers supporting a minelaying operation was a great success but the only one. As an anti U-boat weapon, our submarines attacked ten of them but only succeeded in sinking one. They did, however, delay all U-boats on passage by making them proceed submerged by day as a precaution against attack by our submarines. As raider hunters on the oceans they never got within a thousand miles of either of the pocket battleships and never had an opportunity to prove themselves as convoy escorts. Their efforts, handicapped by political restrictions, to stop the Swedish iron-ore trade with Germany resulted in the sinking of one ship. Although three submarines were lost and two badly damaged by enemy anti-submarine measures, these same measures were unable to drive them out of the areas in which they wished to operate for more than a short period.