Wolverine was ambushed by the Hand and Hydra. Transformed into a killing machine and outfitted with several devices, he battled various other heroes and killed both Hornet and Northstar. S.H.I.E.L.D. was eventually able to deprogram Logan, and he was sent to oppose Northstar, who also had been resurrected by Hydra. While on a mission in the Savage Land, he met the recently reformed Avengers and eventually accepted membership.

Recently, Wolverine unnerved many high level officials, including those of S.H.I.E.L.D., by his sporadic movements in and out of the grid, with the tensions mounting in what seemed to be Wolverine's attempted assassination of the prime minister of Japan. Eventually it was revealed that Wolverine's true target was not the prime minister, but his bodyguard, the Silver Samurai. During an interrogation that began during their battle, and ended shortly after Logan severed the samurai's arm, Wolverine received some more information that led him back to Department H. Despite what he had originally thought, it was not the carelessness of his captors that allowed him to escape; rather, the Winter Soldier seemingly interfered with the operation in such a way that allowed Logan's escape. Wolverine tracked down the Winter Soldier in Serbia for information, but was rendered unconscious after a struggle after which the Winter Soldier revealed that he had earlier murdered Logan's pregnant wife.