Nagasaki, Japan - A millionaire and his chauffeur Ichiro watch their boys play baseball together, when Ichiro's kid gets kidnapped by thugs who were aiming for the millionaire's kid. Ichiro and his wife are distraught, but after weeks of no clues, and no help from police, they call in Wolverine.
Logan agrees to meet the kidnappers with the ransom, and waits in a graveyard for them. He reminisces about how much he hates Japan these days - it reminds him of his lover, and his past, where for one time in his life, he was free of his emotional pain only to have it return twice as bad. A short, fat, Japanese man approaches with two armed bodyguards, offering conversation about the curiosity of a Christian graveyard in the middle of Japan - a product of Spanish missionaries. Logan carries two duffel bags for the ransom, but demands to know where Ichiro's boy is. The fat man says that he is safe, but asks who the gaijin standing before them could be - they were not expecting an American. Wolverine informs them that he is Canadian, but doesn't reveal who he is. He hands over the duffel bags - they are not filled with ten million American dollars, as demanded - but with t-shirts. The fat man angrily asks if this is supposed to be a joke. Wolverine tells him it is more of an insult.
Ninjas begin flooding the graveyard to attack Wolverine. Logan stabs, slashes, decapitates, and disembowels his way through dozens of ninja assasins - who, he finds, have actually been dead for sometime, as their noxious green blood spills onto the ground. He realizes these are probably resurrected Hand ninjas. Wolverine realizes that this setup was probably orchestrated by Ichiro himself.After destroying the lot of them, he goes back to the ringleader, who begs for mercy, and demands to know where the kid is. Right then, a sword cuts through Logan and the leader, killing the man and leaving Logan dazed. It is Gorgon, a man in a red robe, who claims that the child has been fed to the pigs. Wolverine is knocked out by his sword.
A week later - Shadowcat goes to the home of Ichiro and his wife, who are crying over the loss of their son. Ichiro tells Kitty that his son collected birds eggs, and that they placed his collection in an altar to the boy on a windowsill. Ichiro apologizes for his accent and his frequently breaking down to cry. He says that Logan left a week ago to find the child, but has heard nothing since. Kitty assures Ichiro that Wolverine has been in bad situations before, and sometimes disappears for weeks before turning up at unexpected times.
Minneapolis, Minnesota, a month later - S.H.I.E.L.D. investigates a church where a mass murder has taken place, where they find evidence of an intricate HYDRA plot to kill 16 prominent superhero figures, including Wolverine, Reed Richards, Captain America, and Charles Xavier. Fury tells Elektra that the man behind everything is Gorgon, a Japanese man with superstrength and skills of a HYDRA ninja-master - explaining Wolverine's apparent death in Japan a month ago. Gorgon was a mutant gang leader in Kyoto before rival gangs killed him. The Hand resurrected Gorgon three weeks later. Gorgon is known to have been working with a splinter group of the Brotherhood called the Dawn of the White Light - a group who had recently formed a pact with HYDRA and the Hand. Fury asks Elektra if she's sure she can help. Elektra insists that she will make the time to find Wolverine, though this whole incident seems suspicious. A soldier approaches, and relays the message that Wolverine has been found in South America.
Fury and Elektra take a S.H.I.E.L.D. aircraft carrier to South America, where they obtain Wolverine's battered body, which was abandoned in an open pit. Fury assumes that they left him for dead, as there is no information anywhere regarding how he was detained for so long. Logan remains in the sick bay, regenerating massive wounds. Logan is starting to wake up, but hears a voice in his head ordering him to kill the doctor. Wolverine is confused. The doctor chastises him for never seeing her again after a mission four years ago, but mentions that she likes how he's wearing the costume again - as mutants just look scary in black biker gear, where the superhero costumes are more calming to the public, not to mention sexy. Wolverine hears the voice insisting that he get up and kill her now - he works for HYDRA. Without warning, as the doctor gets him a drink of water, Wolverine sits up and stabs her through the heart.
Above deck, an officer watches the security camera trained on Wolverine, and calls over his comrades to look at the monitor. However, the camera is soon knocked out, and the entire security grid shuts down a moment later. The S.H.I.E.L.D. officers order Elektra to shut herself in an empty room, but she ignores them, and removes her trenchcoat to prepare for a fight. The power grid fails. The officer explains that it will only be 25 seconds before the backup power comes online, but Elektra tells everyone to get down - she knows that Wolverine is in the room.
Above, Logan has put his yellow X-Men costume back on, and greets Elektra with open claws.