Captain America successfully managed to board and take control of one of HYDRA's submarines, the Leviathan, and used it to infiltrate the secret HYDRA U-Base together with the Howling Commandos, as their intelligence suggested HYDRA was building a giant weapon inside it.
Steve Rogers and his men prepared to exit the submarine and attack the HYDRA security contingent that would be standing guard at the base, but they found the submarine dock was empty. Dum Dum Dugan proposed to search the base in case the soldiers were just hiding, and ordered Gabe Jones and Jacques Dernier to search the left corridor, and James Montgomery Falsworth and Jim Morita to search the right corridor.
Dugan planned to search the middle corridor with Captain America, but he already departed alone while Dugan was speaking, making him remark that Captain America's skull was thicker than his shield. Captain America found an old laboratory, but no trace of the super weapon they were sent to destroy.
Captain America examined some diagrams of the mythological Lernaean Hydra when he was contacted by Falsworth, asking for help as he and Morita had been attacked. Captain America rushed to their aid, and he found that Morita and Falsworth had been trapped by a huge tentacled creature.
Captain America attacked the creature with his shield, cutting one of the tentacles, but the creature quickly regenerated two tentacles in its place. The creature dragged Morita and Falsworth to a flooded section of the base, leaving Captain America unable to follow them.
Rogers went back to the laboratory, where Dugan, Jones and Dernier had been studying the diagrams of the creature. Rogers swore he would save his commandos. Jones managed to discover that the base was dedicated to experiments regarding cell regeneration, experimenting on soldiers to literally apply the HYDRA motto "cut off one head, two more take its place".
Dugan theorized the creature must have attacked and killed the base's staff, as he searched the rest of the base using the plans of the whole complex and none was to be found. Dernier proposed to plant explosives on the floor to drop the ceiling over the creature, who had transformed the sub-basement into its lair, but Dugan acknowledged they needed to rescue Falsworth and Morita first.
Captain America swam to the sub-basement, having 30 minutes to rescue his men before the ceiling collapsed over them, and Jones contacted him once he emerged from the water. Jones informed him that, according to the lead scientist's journal, an underwater earthquake damaged the base, flooding the sub-basement, and the Hydra Serum they were testing infiltrated to the base's water supply.
Rogers still was concerned about where the creature came from, and how it managed to devour the entire staff of the base without a single survivor, but he managed to find the creature and requested radio silence. He followed the tentacled beast to its lair, but the creature was luring Captain America straight to a trap, using Morita and Falsworth as living bait.
The creature attacked Rogers, who defended himself cutting the tentacles that were trapping Falsworth and Morita before it could devour them. Captain America continued speaking to the creature as it regenerated, guessing if it had been a regular jellyfish that was affected by the serum, and ordered Falsworth to take Morita out of the sub-basement to avoid the incoming explosion.
Dernier contacted Rogers to inform him the charges would explode in two minutes, but the creature wrote the words "help me" in German in one of the walls. Rogers realized the truth about the creature and shielded it from the explosion.
The Howling Commandos went on to check if Rogers was unharmed, and he explained the reason why he saved the creature. Captain America managed to realize that the creature was actually the entire base's staff, having been merged together by the serum, and it was only trying to ask for help in the only way he could.
Rogers revealed his intention of taking the creature to Howard Stark for help, making Dugan point that HYDRA would surely not do the same in case an Allied soldier had been affected that way. Captain America revealed that precisely that difference was what made their side the right one.