In the private study of his mansion, Professor Charles Xavier asks his student, Wolverine, what it is that he fears. Logan replies that it's himself, like he doesn't know who he is anymore. When asked why he feels that way now, he claims he doesn't know, and if he did, he'd handle it. Xavier brings up Proteus, and Wolverine grips his hand hard against the chair, as he recalls his encounter with the reality-warping mutant. A quick flashback to the specific point in "Proteus (1)" shows the energy being form of Kevin MacTaggert tearing Logan apart at a molecular level, melting him a pile of goop, and once he's restored to normal, he's left sobbing and disturbed. Wolverine denies that being the cause to the Professor, claiming he's already worked through that. Xavier then brings up the revelation of his Weapon X brainwashing, asking if that distressed up. Logan's eyes show a great deal of fear, as he flashes back to the flashback in "Weapon X, Lies, and Video Tape", where he was being forcibly trained to become a sleeper assassin. Softly trying to pass off the situation, by telling the Professor that he's got a lot of memories, and so what if some aren't real, he then recalls the end of that episode, when Silver Fox, confronted with the possibility that the two of them really were a couple once, fails to care, and departs. Xavier asks if his problems are about Jean, and a flashback occurs to the tense moment between Logan & Jean Grey from "Captive Hearts", when they got too close for comfort together. He points out that when Wolverine first came to the school, he was wild, confused, and out of control, and he learned to harness a rage as he found a home there. Scenes from "Till Death Do Us Part (1)" (Logan cutting loose in the Danger Room) and "Captive Hearts" (Professor X and Jean use their telepathic powers to quell Logan's mind), play as he says this. Sensing he is no happier, Xavier asks what he's afraid of doing. Logan explains that when he used to go berserk, he was an animal, with no direction or purpose, and the X-Men gave him a reason to back off or not to fight, but now, that feeling's not there anymore. Professor X is taken aback, asking him to consider what he's saying, until Wolverine tells him that he wanted to waste a kid today just for cutting him off in traffic. The scene semi-fades to earlier in the day, when, driving through the city in his jeep with Jubilee, a black car swerved roughly against them. Once at a stop light, Logan jumped out, ripped off the car's door, pulled out the driver, and popped his claws, preparing to gut the teenaged boy. Jubilee tried to stop him, and ended up getting knocked over, nearly hit by a car pulling up behind them. Nearly harming the girl didn't even bother him, and as the flashback ends, he admits he didn't care, noting how even animals care about each other. Wolverine doesn't know what's missing inside, or how he lost it, but there's only one place he might be able to regain it. He rises to his feet, and gently declares that he's leaving the X-Men to go to Japan. This causes Xavier's jaw to drop.
A short time later, a yellow taxi pulls up to the X-Mansion, and honks its horn. In his room, Wolverine packs up his backpack, and upon putting it up on, he faces a mirror. Within it, he sees the mutant known as Nightcrawler, repeating words he said to him back in the episode "Nightcrawler", to open his heart, and asking if it would hurt so much to see the world through different eyes. Logan shakes his head, and tells his pal that he wishes he could, and when the reflection of Nightcrawler changes to that of his enemy Sabretooth, laughing deeply at his plight, he concludes that his eyes see himself too well. He pops his claws, smashes the mirror, and shuts the mocking image up permanently. Jubilee enters the room, telling him that his taxi has arrived, and with her voice nearly breaking from emotion, she asks him why he has to leave. He grabs her by her collar, and angrily reminds her that he didn't care what happened to her or that kid. He lets her go, and pushes her aside, prompting a near-crying response that the Professor helped him before, and can do it again, promising the whole team will help. Logan thanks her, but admits that right now, he's not fit to be one of the X-Men. One jumbo jet-ride later, Wolverine ends up back in Japan, remarking to himself that there's a place he was happy once, a simple world where he knew how to live, and maybe he can find what he's looking for there. He arrives at a very old-fashioned and traditional Japanese village, and immediately upon climbing the steps to the central courtyard, an old, bald monk greets him "Yookoso, Logan-san", asking how many years have passed, and mentioning that he'd been expecting his return. Wolverine nods and bows, thanking the man he calls Master Oku. He glances over to the half-finished structure, commenting how they're still not done with their new temple. Oku claims they do what they can, and when he spots the old-style hammer & saw being used, he quips that with those tools they'll be doing it for a long time. The Master replies that they've nowhere to go, so are in no hurry, which makes Logan lament how he feels like he's been in a hurry ever since he left Japan. He asks if he'd mind if he picked up where he left off, and bowing with his hands clasped, Oku says that it would be an honor. Two monks are struggling with a tall wooden pillar, nearly losing their grip on the vertically placed log, until Logan notices their need, and rushes over to assist in keeping it upright, and getting it locked into place. Watching this, Master Oku mentions how perhaps building the temple will aid him in rebuilding his soul.
As the sun rises in the land of the rising sun, Wolverine sits in a meditative stance, on a cliff overlooking the sea. Later, he pushes a wheelbarrow filled with stones into the temple, dumping them out, to be sorted by the monks. Later still, he sits alongside his fellow workers, and as they eat their meals with chopsticks, he sips tea patiently, decked out in a karate gi. And when the sun sets, a monk bangs the bell, signaling the end to the work day. Though the other monks halt production on the temple, Master Oku has to tell Logan to stop, since he claims he isn't tired. The villagers have prepared a feast, and it would dishonor them to keep them waiting, so Wolverine sets down the wooden board he'd been working on, and follows Oku down the long flight of hillside steps, to the village below. As he walks beside the Master, he notices all of the people giving him strange stares. Oku claims they're just curious about the different-looking person, and soon introduces him to the village elder, Yoshida, who recalls having seen him working at the temple, and if the monks can welcome him, then so can he. He tells his daughter Kisara, a young woman in a pink dress, to show Logan to his table at their restaurant. On the way in, a man on a motorcycle pulls up, revealed to be Kisara's brother, Soichi. Yoshida scolds his son for not having been with the fishing fleet that morning, and Soichi argues that he had been training, calling himself one of the few who have the courage to fight their enemies. The elder calls such a thing forbidden, planning to do what they've always done and pay them. Protesting, Soichi grabs Yoshida's collar, only to get grabbed himself by Wolverine, who tells him to respect the elder, When the young man pushes him away, saying he only respects those who've earned it, Logan's instinct is to pop his claws. He grips his fists, but manages to hold back, and backs down, agreeing with him, apologizing for interfering. Wolverine resumes walking off with Kisara, prompting Soichi to call him a coward, telling him to go back to the temple and hide. Master Oku remarks that it's often the braver man who chooses not to fight.
Meanwhile, just behind the X-Mansion, a Mini-Jet takes off from the hidden hangar, skimming across the lake in a rough liftoff. The pilot is a somber Jubilee. As Professor Xavier reads the note she left him, a short time after she's fled, her voice narrates that she doesn't know why Wolverine left, but knows he's alone and unhappy. She peeked at his personal file, and though it took a while, she thinks she knows where he went in Japan. Jubilee tells Xavier in the note that she has to go and try to help Logan, or she'll never forgive herself, and she knows the Professor will understand. The next day in Japan, Wolverine lifts a large stone slab, his years of physical combat having prepared his muscles well for such a task. Master Oku informs him of the need for more timber for the temple roof, and he humbly agrees to get them. When asked if he'll need a saw, he chuckles slightly about that spoiling the fun. Once out in the forest, Logan pops his claws, and cuts down a whole tree, calling out "timber" as it topples. Suddenly, a man in a silver-armored samurai warrior costume appears in midair, right above the trunk of the freshly cut tree! He asks the mutant what he's doing there, first in Japanese, then in English, as he slowly floats to the ground. Wolverine replies, in English, then in Japanese, returning the question. He claims to be the Silver Samurai, and that the people of this province know to fear him, telling him to stay out of matters that don't concern him. Not that it was any of his business, Logan tells him that's just what he had in mind. Silver Samurai calls his decision wise, and wises he lives to benefit from it, before teleporting away again. Back in the village, a whole gang of Asian men on motorcycles pulls into the town square, the leader of the pack, named Takaki, parking right in front of Yoshida. He warns them that the tribute owed to the Silver Samurai is due in three days, and the elder laments that it has been a bad year for them, as they can scarcely feed themselves. Claiming that their master can't eat their excuses, Takaki demands they pay up in three days. Soichi cries out that they will no longer pay his extortion, and grabs the man, trying to pull him off his bike, and though he does, another biker zooms past, knocking him down as well. Once Takaki recovers, he prepares to make the "peasant" pay for his actions. Silver Samurai teleports in behind him, stopping his attack on Soichi, telling his servant that they don't need a martyr. He then tells Yoshida that he disappoints him for not having better control of his villagers, and when they return in two days, the payment must be doubled. Silver Samurai has Takaki and his gang leave the town a reminder.
Soon, Wolverine is heading back from the forest, lugging a load of logs, when he spots smoke on the horizon, instantly realizing it's coming from the temple. He drops the wood, and races ahead, finding the monks standing outside the burning temple. Kisara is also there, urgently telling Logan that Master Oku is trapped inside! He darts into the flaming structure, calling out for Oku, as he uses his claws to cut into the ablaze debris crashing around him. Once Wolverine reaches the meditating elder, he picks him up, and carries him out to safety. When asked how this happened, Kisara tells him the whole tale of Silver Samurai demanding a tribute from the villagers every year. Logan gets the picture, calling this the old protection racket, samurai style. Kisara says that this year, they have no money to pay, since they are merely fishermen, and thus, the bullies will destroy their village. Glancing at the helpless and poor villagers, Logan grips his fist and lets loose a low growl, realizing in frustration how it never ends. He heads off alone, and as the temple continues to burn, Wolverine stands on the beach, gazing silently at the crashing waves at sunset. Kisara soon rushes to him, begging for his help, as Soichi is organizing the village to fight the bandit. Logan refuses, telling her he came to find himself, not to fight. She points out how the people aren't trained to fight, and lack weapons, leading to him asking her what Master Oku would have said. Kisara admits he'd have said no worldly possessions are worth the risk of one's life, which Wolverine says to tell to the villagers, as he walks away from her. She then comments how Oku would have also said that inner peace is found not by avoiding conflict, but in serving your true nature. Logan pauses, looks down at his hands, rubbing them briefly, and repeating the remark about his true nature. He pops his claws for a moment, and proclaims aloud that he wishes he knew what it was.
The next day, at the temple, Jubilee shows a picture of Wolverine to a monk, and attempts to overcome the language barrier by talking as slowly as she can. It doesn't work, and she's unable to get a positive response from the man. In the woods outside the village, Silver Samurai orders his motorcycle-riding lackeys to destroy any of the "fishmongers" who fight back. Takaki asks his master what one small village matters, and the Samurai compares each of the fearful villages to links of a chain, and how if one resists, better to make an example by crushing them than let the whole chain be broken. Inside the village, Soichi rallies a less-than- enthusiastic mob, armed with gardening tools, urging them to fight back against the evil Silver Samurai. Yoshida tells the boy how foolish it is to force fishermen and farmers to face armed fighters, and he declares that it's better to die defending themselves than to live in fear, and how their children shall not suffer as they have. Wolverine arrives, hauling more logs, and when Soichi tells him to go back to hide with the monks, he states firmly that he doesn't hide from anyone, and he's fighting his own battle as they speak. But he agrees that they either stand and fight, or they'll be kissing the Samurai's backside forever. The mob of villagers grows more confident, cheering for no more tributes. Yoshida whines about how Logan is repaying them by helping bring destruction to the village. He turns and walks away, unsure of himself more than ever. Soon, the villagers set traps on the forest road, large battering-rams in trees; nets filled with fish, hoisted up out of sight; trenches dug into the ground; balloons prepared by Kisara and the other women; and a wooden wall overlooking the sea. That night, Wolverine stands in front of the temple, silently contemplating. Master Oku, looking no worse for wear, approaches, intuitively commenting that he's deciding how to act tomorrow. Logan tells him that the villagers will be slaughtered tomorrow, and he came there to get away from fighting, to be like him, and just wanting to live in peace. Oku asks him if he truly does, since peace comes with purpose, noting that his faith gives him his. Wolverine angrily calls ripping up people no purpose, only to have the master claim that protecting and caring for people is, and how like many, perhaps he seems himself as less-well than others do, suggesting that he look at himself through new eyes. His voice breaking from frustration and distress, Logan tells him that he wants to do that so much, and when he turns around to face Master Oku, he finds the elder monk gone, as if he was never there to begin with.
A short time later, Wolverine slumbers unsoundly on his futon, tossing and turning wildly. His mind is filled with images from previous episodes: the eyes of Evil Morph; the eyes of someone looking at Vindicator; Logan strapped to a table from "Repo Man"; Logan in the Weapon X tube during his flashback from that episode; The "Professor", Lady Deathstrike, Omega Red, Sabretooth, Mr Sinister, Jean Grey kissing Cyclops; Sabretooth claiming he can't take care of his woman from "Weapon X, Lies, And Video Tape"; attacking the Cyclops-robot in the Danger Room from "Till Death Do Us Part (1)"; and random images of Wolverine snarling, growling, and generally acting like an animal. He even proclaims that he's not an animal, and when he sees a puddle of water in a rock, showing the reflection of Sabretooth. Kisara touches the water, rippling the image until it becomes Logan, as she tells him to look deeper, that he is just himself, and no one else. He smiles, and touches her hand warmly. This ends the cacophony of nightmares, and Wolverine's discomfort, as he rolls over, and sleeps the rest of the night far calmer than before. The next morning, the motorcycle bandits race along the wooded road to the village. A lookout sentry alerts the villagers to their arrival, setting into motion their intricately laid plans. First, the battering-ram logs slam into several of the bikers, knocking many of them aside. Takaki, sword in hand, vows to make the pig farmers pay for that. Next, they find a large tree trunk blocking the road, forcing a detour to a secondary road. There, several more of the motorcyclists discover the hidden trenches in the path, crashing into the holes without warning. A pair of children giggle at the plight of the bullies, and the few who crawl out hear them, and approach the tree they're hiding in. This allows the boys to pull a rope, releasing the net filled with fish, knocking the men right back into the hole! Another couple of bikers pull up, and spot the boys, drawing their guns in an attempt at revenge. Though Wolverine is rushing to the scene, Master Oku ends up there first, appearing suddenly, and assuring them the children won't hurt them, offering himself to be attacked instead. One prepares to blast him, when Logan claws off the front of his gun, doing the same to his partners, warning them not to touch Oku. One tries to lunge at him, Wolverine grabs the man and hurls him into the other two, allowing the bruised bandits to flee in terror. Oku recovers from his fall, with help by Logan, who asks him what he's doing there. The master says they all fight in their own way, and noting his popped claws, gladly points out that he seems to have rediscovered his own.
The remaining bikers reach the village square, finding the town empty. Takaki claims the cowards have fled, when he and his men get a surprise greeting of multiple falling blocks of wood, being dropped by the specially rigged balloons floating overhead! They recover and drive down to the beach, scaring off the children responsible for this assault, following them down near the wall of wood built the previous day. Atop it, the kids are alright, safely out of the bullies' reach, and with the bikers all together in one small space, a villager breaks a seal, sending this makeshift dam collapsing, and sending a rushing river of ocean water barreling toward the bullies! They're wiped out from their bikes, and are the center of attention at the shallow section of the man-made lake, being laughed at the by villagers, pointing their fishing spears at the men. One of the bandits pull his lasergun on them citizens, only to be told to leave them alone by Jubilee, who blasts him with her powers, ridding him of his gun and making him wetter. She races down to the villagers, figuring if fighting's going on, then Logan's got to be around. Kisara tells her that if she's his friend, she should come with them since he needs their help, and she anxiously does so. In the center of the village, the rest of the villagers have the remaining bikers surrounded. Takaki is unfazed, prepared to deal with the ignorant peasants, as he calls them. They rev up their bikes and race through the small crowd, breaking free of the ambush, when Soichi hurls a spear at their leader's motorcycle, busting the tire and hurling him into the muddy slop of the local pigpen! The pig sniffs him, and turns away in disgust, something which is noted by Soichi when he picks Takaki up, and displays the defeated bandit. He tries to make the peasant pay for laughing at him, but Soichi takes control of the situation, and flips the muddy bully aside with ease. The Silver Samurai, with his katana blade drawn, causes the crowd to disperse as he confronts the young man, asking if he can do as well against him. He slashes at Soichi, but his blade is blocked by the adamantium claws of Wolverine, who tells him he's fighting the wrong guy, calling him a "pretty boy". When Logan tries to punch back, the Samurai teleports out of the way, and pops up behind him, slashes into his back, and does the same again when he turns around to face him. Wolverine wants to let his rage take over, but urges control over himself, to use his head for a change. He lunges at Silver Samurai again, but this time, flips backwards, ending up right behind the warrior when he teleports in to where he thinks Logan will be standing with his back to him. This leaves him open to getting his own trick used against him, Wolverine clawing his belt and lifting him into the air, and using his other set of claws to dispense of the Samurai's katana. Slashing into the red sunburst design on the warrior's chest, which causes a depowering sound as if it were the source of his teleportation, Logan drops Silver Samurai, where he falls to his knees in dismay. Soichi urges him to finish the villain off, and though Wolverine thinks he deserves as much, the villagers stood up to him, and that'll ensure he doesn't bother them or any other village again. Silver Samurai walks off with his head hung low, dishonored and disgraced. A familiar voice calls out Wolverine's name, giving him quite a surprise when he sees Jubilee with Kisara, who claims his supposed friend helped them. Jubilee mentions how she feels his leaving for Japan was her fault, and Logan denies this, saying it was just something he had to so.
Later, the temple rebuilding continues, this time being worked on by the people of the village, instead of just the monks. Master Oku assures Logan it will be completed without him, and Wolverine finally realizes temple-building isn't his job, since they all fight in their own way. Soichi smiles, bows, and thanks Logan, only to get a pat on a shoulder, as he humbly tells him there's no need. Kisara does the same, but gets a kiss on the lips in return, as he denies her thanking, instead thanking her for helping him. Wolverine departs, waving goodbye to Kisara, Soichi, and Master Oku, only the former of which returns the gesture. Jubilee hurries along beside Logan, asking him what she missed, what was with the biker boys, the "big doofus with the shiny metal outfit", and the babe, noting that the two of them sure seemed to have gotten friendly. They continue walking along, with her mouth going much faster, telling him how tough it was to find him, since nobody speaks English, and she remarks that you'd think they'd notice a guy with big claws. Wolverine's renewed inner-peace is surely tested by his companion, and it seems to be holding up quite well.