Working with the Gorgon, Baron Strucker used Wolverine to steal plans for inventions made by Reed Richards with potential use as weapons of mass destruction. Wolverine was used for various other attacks on banks and public areas. Announcing he was going to get a partner, Wolverine walked into a trap set by Elektra and SHIELD when he tried to kill Daredevil. Elektra was captured by the Gorgon to be used as another Hydra operative. Daredevil killed all of Wolverine's Hand ninjas and accidentally impaled him on a sword. In a moment of clarity, Wolverine revealed that they were going to kill the President of the United States. Wolverine was quickly teleported back to the Hydra base.
Sneaking into the Xavier Institute For Higher Learning, Wolverine manipulated Rachel Summers into using Cerebro to kill the President. He threatened to set off a Terraformer he was using as a bomb if she didn't. Using Cerebro to learn how to dismantle the bomb from Reed Richards, Rachel alerted the X-Men to Wolverine's presence. Wolverine tried to escape, killing several SHIELD agents and Northstar before he was captured. Hydra upped the ante, killing and resurrecting several villains for their cause. Baron Strucker was killed for his failure with Wolverine and the Gorgon took his place. Hydra attacked the Heli Carrier, trying to spring Wolverine free and destroy SHIELD. Wolverine was deprogrammed quickly by SHIELD scientists and prevented the attackers from killing Nick Fury.Making it his goal to stop Hydra, Wolverine fought the Hydra controlled Northstar and his mutant companions. He won with the help of Sentinels he had taken from SHIELD. Next, Wolverine attacked the Hand base. He killed almost all of them with the help of Elektra, whose evil actions had been part of a trick to learn all the whereabouts of Hydra's secret bases. SHIELD simultaneously destroyed all of them. Wolverine and Elektra fought Gorgon, who easily defeated them both. Gorgon went to the hospital where Nick Fury was healing to kill him. He was stopped by Wolverine. In a final battle, Wolverine was able to kill the Gorgon.