Upon completion of boats "S 128" and "S 135" they were put under control of the 2. SFltl for one operation. During this "S 128" was lost on February 23rd 1944 due to a collision with "S 94" (Oblt.z.S. Bosenuik). 

The infavourable weather resulted in the flotilla's entering Reval on 15.02.1944 only with seven boats. A change of weather occurred with icing of the Gulf of Finland, so that the boats were taken back to Libau (Liepāja). 

On March 7th 1944 the flotilla transferred with tender "Carl Peters" (Oblt.z.S. Reuthal) to Reval-Kopli and end of March into the Finnish skerries off Luwista. The flotilla was mainly operating against pickets and small boat units since there were no torpedoworthy targets. Thus it came to frequent gun fights.

On May 14th 1944 the 6. SFltl sank the Soviet guard "MO-122" in a fight east of the island. On May 26th 1944 the flotilla reported the sinking of a guard again.

After  the Allied landing in the Normandy had taken place on June 6th 1944 and  14 S-boats had been victims of an Allied bomb attack at Le Havre on June 14th 1944, the 6. SFltl was ordered back to the western front.  

On June 15th 1944 the 6. SFltl left Helsinki with eight boats. "Carl Peters" stayed at Reval, "S 79" in the shipyard at Libau. On June 19th 1944 Cuxhaven was entered. The weather permitted the transfer to Ijmuiden not earlier than on June 25th 1944. "S 39" had an engine failure en route and was dismissed to Cuxhaven together with "S 135".

Since the SKL had requested F.d.S. to make proposals how he could imagine an S-boat presence in the Baltic Sea, he proposed to form a flotilla of eight boats with skull-bridges (Kalottenbrücke = armoured bridge) from the stock of the S-Boat-School-Division (S-Boot-Lehrdivision).

In addition to the already existing two S-Boat-School-Flotillas the 3. S-Schul-Fltl (Kptlt. Siems) had been formed on 15.06.1944. The 10. SFltl (Kptlt. Müller, K.) having been formed in March 1944 was under training with the older boats "S 65", "S 67", "S 80", and "S 85" and the new boats "S 183", "S 185", and "S 191" based on Swinemünde. The boat "S 192" commissioned on June 7th 1944 was still at Travemünde for remaining works.

"S 65" ona training voyage in the Baltic Sea - Picture: Archives E. Skjold

On June 15th 1944 four Finnish S-boat-crews arrived at Saßnitz, which were to take over the boats "S 64", "S 83", "S 99", and "S 117". Also the boats "S 86", "S 89", "S 92", and "S 98" were planned to be delivered to the allied Romania. The handing over of eight boats in this phase of war was a bigger bleeding. The political and the military development, however, did not let it happen, the boats foreseen for Romania stayed in posession of the KM. The boats already on the Danube were stopped and integrated preliminarily into the Danube-Flotilla before they were transferred back to the Baltic Sea. Boats "S 92" and "S 98" were still at Linz when they were stopped on August 24th 1944 with engines just mounted, the boats were taken apart again and transported back to Germany. "S 86" an "S 89" were already at Orsava when they got the order to return. On August 25th 1944 they were assigned to the Danube-Flotilla. On September 21st 1944 the boats were at Linz. "S 92" and "S 98" were assigned to the 5. SFltl, "S 86" and "S 89" to the 1. SFltl, and the four "Finland-Boats" ("S 64", "S 83", "S 99" and "S 117" were assigned to the 2. S-School-Fltl.

"S 85" in a harbour in the Baltic Sea - Picture: Archives E. Skjold

The SKL insisted in detachment of a S-flotilla to the Baltic Sea. F.d.S. finally detached the  5. SFltl, of which only "S 112" was still in service. The 5. SFltl (Kptlt. Holzapfel) had practically to be newly taken into service on July 3rd 1944. It got the boats "S 65", "S 67", and "S 80" from the 10. SFltl. From the  2. S-School-Fltl came "S 120" and "S 68"; from the 3. S-School-Fltl came "S 85". As tender the 5. SFltl got "Hermann von Wissmann" (Kptlt. Jakobsen).

The 5. SFltl with "S 65", "S 67", and "S 80" together with the tender left harbour to July 12th 1944 to transfer to Finland. The crews were poorly trained. The boats were marterialy not 100 % ready for action. "S 85" remained behind with propeller problems. As berth the bight west of  Strømslandet was planned.

"S 68", "S 110", "S 116", and "S 120" were at Stettin for engine overhaul. End of July "S 68", "S 85", and "S 120" transferred from Libau to Helsinki, "S 110" and "S 116" were fitted with a 40-mm gun at Gotenhafen (Gdynia).

Iniitially the boats operated from Helsinki, then from Hamina, without finding worthwhile targets. Mostly they were employed in picket and mining service. 

On August 30th 1944 the 5. SFltl was ordered to drop depth charges on the sinking position of "U 250" in order to destroy the boat. The submarine had, however, already been salvaged by the Soviets. On the way back "S 80" (ObStrm. Borkenhagen) run into a mine off Viborg. Killed in action were: Matr.ObGefr. Waldemar Riegel, Masch.ObGefr. Hans Mischer, Masch.ObGefr. Hans Rugelies, Masch.ObGefr. Hans Tittel, Matr. (SOA) Egon Voigt.

On September 1srt 1944 the 5. SFltl consisted of the following boats:

On September 2nd 1944 the Finnish prime minister declared the breaking off of the diplomatic relations to Germany and requested that Germany should withdraw its troops from Finland. Therefore, the 5. SFltl and "Hermann von Wissmann" transferred to Baltischport (Padilski) on September 2nd 1944. On September 14th 1944 the offensive of the Soviet army against the Army Group North (Heeresgruppe Nord) commenced.

On September 14th 1944 the 5. SFltl left harbour with four boats ("S 116", "S 85", "S 120", and "S 110") to mine the base of the 1. Finnish SFltl. The mines were laid as planned off Kotka, however, the Finns had observed the mining operation and could therefore not be hindered to leave Kotka. The mining was a measure within the operation "Tanne Ost", the occupation of the island Hogland. The German landing corps, however, was forced to surrender to the Finns. The attack plan reached the 5. SFltl so late that it could not prevent the Finns S-boat attacks.

On September 15th 1944 the 5. SFltl undertook a sortie from Reval in direction of Hogland, without Soviet ships coming in sight. A Finnish S-boat group passed without a fight developing.

On September 17th 1944 navy personnel was recovered from the island Pein Tytarsaari by the 5. SFltl, among them the commander of the 7. gunboat-flotilla, which had taken part in operation "Tanne Ost".

On the sme day the OKM ordered F.d.S., to dispatch the 2. S-School-Fltl immediately for operations in the east. The flotilla reported boats and tender "Tsingtau" ready to proceed on September 19th 1944. The transfer was ordered not earlier than on September 29th 1944. 

On September 18th 1944 the boats of the 5. SFltl escorted the hospital ship "Oberhausen", a German-Finnish POW-exchange was to take place, but the Finnish boats did not appear.

On September 22nd 1944 Reval (Tallinn) was given up and the 5. SFltl transferred to Windau (Ventspils) after they had mined the harbour-entrance of Reval..

On September 29th and 30th 1944 the two flotillas laid mines again. A sortie into the sea area off Dagø and Ösel remained without enemy contact. 

On October 1st 1944 the boats "S 64", "S 76", "S 81", and "S 135" were available at Windau. When the commander 2. S-School-Fltl, Kptlt. H.H. Klose, entered Windau, the newer tender "Hermann von Wissmann" was transferred back to Germany because of the high air threat. The 2. group of the 2. S-School-Fltl continued training based upon Swinemünde.

The island Dagø had to be given up on October 3rd 1944, on September 5th 1944 the Soviets landed on Ösel. On October 8th 1944 the 2. S-School-Fltl mined the Pernau (Pärnu) Bight with 32 LMBs.

In the time following the 5. SFltl and the 1. Group of the 2. S-School-Fltl performed frequent common reconnaissance voyages and laid mines in many nights.

On October 22nd 1944 the 2. S-School-Fltl together with the 1. R-Fltl laid barrier "Olympia I" (40 LMB) while the 5. SFltl laid barrier "Olympia II" (32 UMB). 

 During a sortie into the Bight of Riga "S 110" was attacked by a Soviet aircraft and had to take many hits on  October 26th 1944.

During September and October 1944 many Soviet ships were lost on the barriers: a submarine, four minesweepers, three small minesweepers, three patrolboats, five S-boats, two tugs, and a gunboat.ed off Ösel. 

On November 1st 1944 the boats of the 1. SFltl were widely spread: Only one boat, " S 65", was ready for action at Windau (Ventspils. "S 68" and "S 116" were not ready for action at Gotenhafen (Gedynia), "S 67" and "S 120" at Stettin, "S 85" at Königsberg (Kaliningrad), "S 110" at Danzig (Gdańsk). Of the 2. S-School-Fltl were "S 64", "S 69", "S 76", "S 81", "S 99", and "S 117" ready for action at Windau (Ventspils), "S 83" and "S 113" were at Swinemünde (Swinouśje).

On November 11th 1944 the attack on the peninsula Sworbe commenced. The 5. SFltl performed reconnaissance off Sworbe with four boats in order to find a landing unit which had been reported. They bumped into a unit of six motor gunboats and 14 small vehicles. When they attacked them they got under fire of units that had approached unnoticed. "S 69" and "S 65" attacked the unit sighted first with torpedoes, all failed. "S 68" and "S 116" attacked the other unit. A group of Soviet S-boats intervened in the battle and shortly after six aircraft attacked the boats. "S 68" took some hits, on "S 116" one engine fell out and one man was killed in action. The landing unit was not sighted.

In December 1944 the 2. S-School-Fltl performed three mining operations. Mid December "S 68", "S 116", and "S 120" of the 5. SFltl were ready for action at Windau (Ventspils). "S 65" was in the shipyard at Danzig (Gdańsk, "S 67" was not ready for action at Stettin (Szczecin), "S 110" was not ready for action at Gotenhafen (Gdynja). On 23.12.1944 the flotilla was called back to the west and arrived at Kiel on December 26th 1944 with "S 48", "S 67", "S 85", "S 92", "S 98", "S 110", "S 127" and "S 132". 

On December 21st 1944 the 4. SFltl called back from Norway arrived at Kiel and sailed on to Wilhelmshaven.

On December 25th 1944 also the 1. S-School-Fltl with tender "Adolf Lüderitz" was assigned to front-employment. It was ordered to proceed to Norway.

On the same day the provisional base at Windau (Ventspils) was ready so far, that tender "Tsingtau" could be withdrawn. On the same day four boats of the 3. S-School-Fltl - "S 24", "S 25", "S 105", and "S 118" - transfered to Copenhagen. The other eight boats - "S 68", "S 97", "S 107", "S 108", "S 113", "S 115", "S 122", and "S 123" -  remained at Swinemünde (Swinouśje). "S 21", "S 22", "S 50", "S 101", "S 103", "S 95", "S 120", and "S 82" were in the shipyard at Stettin (Szczecin). The newly formed 1. Section of the S-Boat-Trainingdivision only had "S 19" at its disopsal.

The 1. S-School-Flotilla transferred in January 1945 with "S 62" (Oblt.z.s. Hermann Rost), "S 79" (Oblt.z.S. Herbert Zeiler), "S 90" (Lt.z.S. Gärbers, and "S 133" (Lt.z.S. Günter Schiersmann) with tender "Adolf Lüderitz" to Kristiansand. "S 89" (Oblt.z.s. Jasper Osterloh) stayed KB at Swinemünde, "S 109" (Lt.z.S.d.Res Kopperneck) was getting new propellers at Stettin. The flotilla as "Einsatzgruppe Egersund" was to stay at immediate readiness in all nights other than nights with no German traffic between Kristiansand and Stavanger and nights not permitting S-boat-actions.

At the same time four boats ("S 24", "S 25", "S 105" and "S 118" transfered to Copenhagen. The school-boats "S 97", "S 107", "S 108", "S 113", "S 115", "S 122", "S 123", and "S 68" stayed at Swinemünde (Swinouśje). "S 21", "S 22", "S 50" "S 101", "S 103", "S 95" "S 120" and "S 82" was for different reasons in the shipyard at Stettin Szczecin). 

The newly formed 1. SFltl (Korv.Kpt. Büchting) had been provided with the newly built "S 225" (Oblt.z.S. Behrens), "S 707" (Oblt.z.S. Neumeier), and "S 216" (Kptlt. Seevers) at the outset of the new year. In January 1945 followed "S 708" (Obl.z.S. Karl Silies), "S 218" (Oblt.z.S. Günther Lutherer), and "S 217" (Oblt.z.S. von Dülong). In March  followed "S 226" (Lt.z.S. d.Res. v. Glasenapp).