German torpedo boat Seeadler

At the beginning of the war, the 4th Flotilla was disbanded and Seeadler was transferred to the 6th Torpedo Boat Flotilla where she supported the North Sea mining operations that began on 3 September 1939. On 13, 18 and 19 November, the 6th Flotilla and one or two light cruisers met destroyers returning from minelaying missions off the English coast. Two days later the flotilla patrolled the Skagerrak to inspect neutral shipping for contraband goods before returning to port on the 25th. From 14 to 16 December, Seeadler and the torpedo boat Jaguar made contraband patrols in the Skaggerak, impounding six ships. In retaliation for the Altmark Incident where the Royal Navy seized captured British sailors from the German tanker Altmark in neutral Norwegian waters on 16 February, the Kriegsmarine organized Operation Nordmark to search for Allied merchant ships in the North Sea as far north as the Shetland Islands. The 2nd Destroyer Flotilla, Seeadler and the torpedo boat Luchs escorted the battleships Scharnhorst and Gneisenau and the heavy cruiser Admiral Hipper during the initial stages of the sortie on 18 February before patrolling the Skaggerak until the 20th.[13]

During the Invasion of Norway in April 1940, the boat was assigned to Group 4 under Kapitän zur See (Captain) Friedrich Rieve on the light cruiser Karlsruhe, tasked to capture Kristiansand. They departed Wesermünde on the morning of 8 April and arrived off Kristiansand the following morning, delayed by heavy fog. They had been spotted approaching the city and the alerted coast-defense guns at Odderøya Fortress opened fire on Karlsruhe at 05:32. The cruiser, Seeadler and Luchs returned fire. Neither side inflicted any damage on the other, although several of Karlsruhe's shells missed their targets and impacted in the city. With only his forward guns able to bear and his ships loaded with troops, Rieve ordered them to turn away and lay a smoke screen to cover their withdrawal at 05:45. Shortly afterwards, a flight of six Heinkel He 111 bombers from Kampfgeschwader 4 (Bomber Wing) attacked the fortress. Most of their bombs fell outside the fortifications, but one blew up the western ammunition dump and another near the signal station, killing two men and cutting most external communication lines. Encouraged by sight of the blast from the annumition dump and the numerous hits all over the island on which the fortress was built, Rieve ordered his ships to make another try at 05:55, this time at an angle so that all guns could bear. Accuracy for both sides was better this time, but no German ship was damaged and only a couple of shells from Karlsruhe landed inside the fort, wounding several gunners. With no discernable effect on the Norwegian defenses, Rieve was forced to withdraw again at 06:23. He now conceived the idea of bombarding the fortress at long range where he could use plunging fire to attack the guns from above and Karlsruhe would be out of range of the defending guns. The ship opened fire at 06:50 and Rieve ordered Seeadler and Luchs to steam through the narrows, but the fog closed in before they could get there and he had to cancel his order. The cruiser's fire was generally ineffective, with more shells landing in the city, so Rieve withdrew around 07:30 and requested additional air support.[14]

Around that time a British reconnaissance aircraft overflew Kristiansand, but failed to see the German ships off shore. The naval commander of the area queried the supreme command whether British forces should be engaged or not and received the order to let them pass. He passed that order to Odderøya at 08:05. Rieve made another attempt to force the narrows around 09:00 when the fog briefly lifted, but nearly ran Karlsruhe aground and withdrew again. Getting desperate, Rieve ordered his troops loaded onto four of his small E-boats when the fog began to lift again at 09:25 and ordered them to storm the harbor regardless of casualties. An hour later, the Norwegians spotted the incoming German ships with Seeadler and Luchs approaching at high speed, followed by the four E-boats. They were reported at two cruisers and their approach from a different direction caused some observers to think that they were not German, especially since there had been a rumor earlier of British ships spotted in the Skaggerak. The confusion was compounded when observers reported that they were flying the French tricolor flag, confusing it with a Kriegsmarine signal flag of similar color. This caused the Norwegians to think that they were being saved by Allied ships and their guns did not open fire so the Germans landed without resistance and occupied the defenses beginning around 10:45.[15]

Rieve was under orders to return to Kiel as soon as possible, so Karlsruhe sailed at 18:00, escorted by Seeadler, her sister Greif, and Luchs. At 18:58, one torpedo from the British submarine Truant struck the cruiser amidships, knocking out all power, steering and the pumps. Luchs evaded the other nine torpedoes and followed them to their origin and began depth charging the submarine for the next several hours, joined by the other two torpedo boats. Truant was damaged, but survived their attacks. Rieve ordered his crew aboard the torpedo boats and sent Seeadler and Luchs ahead while he remained with Greif to finish off Karlsruhe with a pair of torpedoes. After the heavy cruiser Lützow had been crippled by a British submarine off the Danish coast on 11 April, Seeadler, Greif and Luchs, among other ships, arrived the following morning to render assistance.[16]

On 18 April, Seeadler and her sisters Möwe, Greif, and the torpedo boat Wolf escorted minelayers as they laid anti-submarine minefields in the Kattegat. The boat began a refit at Wesermünde that lasted from May to August after which she was transferred to France. Now assigned to the 5th Flotilla, Seeadler and her sisters, Greif, Falke, and Kondor laid a minefield in the English Channel on 30 September – 1 October. Reinforced by Wolf and Jaguar, the flotilla made an unsuccessful sortie off the Isle of Wight on 8–9 October. They made a second, more successful, sortie on 11–12 October, sinking two Free French submarine chasers and two British trawlers. The 5th Flotilla was transferred to St. Nazaire later that month and its ships laid a minefield off Dover on 3–4 December and another one in the Channel on 21–22 December.[17]

Seeadler, the torpedo boat Iltis and the destroyer Z4 Richard Beitzen were the escorts for a minelaying mission at the northern entrance to the Channel on 23–24 January 1941. The boat was refitted in Rotterdam, Netherlands, from March to May 1941. She was transferred afterwards to the Skagerrak where she was on convoy escort duties. The boat was again refitted in Rotterdam from December 1941 to February 1942 before rejoining the 5th Flotilla. They joined the escort force for Scharnhorst, Gneisenau and the heavy cruiser Prinz Eugen on 12 February 1942 off Cap Gris-Nez during the Channel Dash. From 12 March to 2 April, the flotilla escorted the commerce raider Michel through the Channel despite heavy British attacks, damaging the British destroyers HMS Walpole and Fernie. The flotilla escorted the commerce raider Stier through the English Channel from 12 to 19 May. In heavy fighting on the 13th, British motor torpedo boats torpedoed Seeadler, which capsized and then broke in half with the loss of 85 crewmen.[18]