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Captain America & Thor: Avengers! is a tie-in of the Marvel Cinematic Universe which featured Captain America and Thor Odinson. However, after the release of Thor: The Dark World the "Citadel of Spires" story can be considered non-canon.
On a mission to a HYDRA base in 1944 with the Howling Commandos (minus Bucky for unknown reasons), Captain America stows away on a small merchant boat, when according to his plan it is attacked by a Hydra sub, the Leviathan, as it is a perfect test target. While they are distracted, the Captain swims to the sub and proceeds to enter and attack the crew, wining it for himself and the Commandos, who anxiously wait in a raft. After finding out where the base is via map, they quietly dock in the base, and on Rogers' count they storm out guns-a-blazin', to find it completely deserted. The team decides to split up in groups of two, all but Cap, having already moved to investigate, leaving Dugan alone. After searching, Cap finds a deserted lab that looks like a war had torn through it. Searching through the notes, He discovers that they were working on creating a literal Hydra beast, just as he receives a call for help from Falsworth and Morita, who the creature has in its grip. Trying to save them, He throws his shield to cut through a tentacle or "head" which like the mythical beast, resulted in two more growing back. The creature then drags the two under water. Rushing to inform the rest, Steve is informed by Jones that all records indicate the experiments were only on people. The remaining team decide to set charges to blow up the base while Cap goes to try and rescue the others. upon finding the creature's lair in a caved in area, the Captain notices several German names scrawled into the wall, and is then told by Jones that more notes reveal that the Hydra scientist thought that the "Hydra serum" got in their water supply, when suddenly Cap comes across the beast, still with Falsworth and Morita, and a fight ensues. the two Commandos escape as Cap stays and fights, when suddenly the beast scrawls "Help Me" in German on the wall. Cap then realizes the beast is the scientists, and with ten seconds until the charges detonate protects it with his shield. The beast lives, and he and the Howling Commandos leave, as he reflects on the horrors of war.