Logan's friendly attitude toward Cyclops came to an explosive end during a training session in the danger room shortly after a battle with Arcade. Criticizing Logan's performance during the training, Scott began, "If this were the real thing..."

"But it ain't the real thing, that's the point!" Logan stormed. "It's a flamin' game! I got news for you, Summers! Wolverine don't jump through hoops for nobody! I handled myself fine when I was on my own! An' I cando it again, too!" And then Logan stormed out.

Later, after returning from the other-dimension world ruled by the warrior king, Arkon, the X-Men flew to Scotland, where they were reunited with Jean - or rather the Phoenix-entity that had taken her form and personality. Soon they faced Proteus, a mutant whose consciousness inhabited the bodies of other people, and who had the power to distort one's perceptions of reality. Logan and Nightcrawler found him while he was possessing the body of a policeman. Proteus unleashed his powers against the pair of mutants, using them as guinea pigs to test his skills.

Logan responded by giving way to one of his rages. Nightcrawler tried to keep his friend away from Proteus, but Proteus was determined to see just how tough Logan was. Nightcrawler pleaded Proteus to show Logan mercy. "My friend is out of his mind! He is sinking to some animal level..."

Proteus would not be persuaded. Using his powers to probe Logan's mind, he turned Logan's inner most fears about himself into living nightmares. He found Logan's long-buried childhood fear of vulnerability and used it to make Logan see himself as brittle, fragile, falling apart. Proteus discovered Logan's subconscious fear of what would happen to him if his healing factor ceased to function, making him visualize himself as a ravaged zombie. And finally, Proteus drew on Logan's intense fear of his own capacity for violence, causing Logan to imagine the pain of tearing himself open with his claws.

But Logan didn't give in to these fears. He overcame them, finally slashing his tormentor with his claws. Then, after Storm entered the fray, Logan learned that Proteus had done more damage to his subconscious mind than he realized. When Nightcrawler urged his friend to go to Storms aid, Logan wasn't able to do it. "I want to, 'Crawler - I'm tryin' to - but I can't!"

Later, between rounds in the battle against Proteus, Cyclops saw Logan sitting by himself, trembling uncontrollably with fear - a man radically changed from the Logan he knew. "He's close to breaking," Cyclops realized. "If he doesn't snap out of his funk, he'll be permanently gun-shy. For Wolverine, that's a fate worse than death."

Cyclops decided to take a dangerous way to snap Logan out of his paralyzing fear before it was too late. nightcrawler asked Cyclops to leave Logan alone, but Scott snapped. "I think the runt's faking ... He's either faking or gutless." Cyclops shoved Nightcrawler aside, and Logan began to seethe with anger. Then Cyclops threw a drink into Logan's face. "We've locked horns from the beginning, Wolverine. It's time things were settled between us. That is, if you're not too scared to fight."

Logan leapt to to his feet, infuriated, and charged at Cyclops. "Bub, the day I'm scared o' you is the day I'd better lay down and die." A frenetic battle between the began, with Logan sinking fast into one of his beserker rages. Thinking and moving as fast as he could, Cyclops narrowly succeeded in staying away from his Logan's claws. Finally, Cyclops called a halt to the battle, and Logan, quickly calming down, realized that the fight had succeeded in shaking him out of his trauma.

This was the turning point in the relationship between Cyclops and Logan. "You took a heckuva risk startin' this fracas, boss, Logan told him. "At the end, I wasn't joshin'. I was in a killin' mood, almost crazy-mad. I ain't thought much o' you in the past, Cyke - as team leader, or as a man. I was wrong." From then on, Logan and Scott were friends. Moreover, since Logan had fallen in love with Mariko, he and Scott were no longer rivals over Jean Grey.

Once Proteus had been defeated, the X-Men returned to their mansion in Westchester County. Yet although Logan had come to terms with Scott's leadership, he now found himself having similar problems with Xavier. Thus, Logan found himself storming out of a Danger Room session, this time feeling that Xavier was treating him like a "kid" or an "amateur" needing training in basic combat methods.

Later, Logan accompanied Colossus, Storm, and Xavier on their trip to Deerfield, a suburb of Chicago (Uncanny X-Men #129) to recruit a 13-and-a-half year old mutant, Kitty Pryde, into the X-Men - someone whom Logan will become extremely close to. The mutant leaders of the secret Inner Circle of the social organization known as the Hellfire Club had also learned about Pryde and they were determined to get a hold of her themselves. The Inner Circle was a conspiracy that intended to amass enough economic and political power to dominate the world.

While Xavier spoke with Kitty's parents, the other three X-Men took her to a nearby malt shop. Logan was itching for a fight after the episode in the Danger Room. So when the shop owner objected to Logan's reading a magazine without paying for it. Logan smiled nastily and nearly lashed out at him.

But Logan never got the chance, for just then the shop was invaded by Hellfire Club mercenaries in armored battlesuits, under the direction of Emma Frost, the Club's White Queen, who took the three X-Men prisoner.

Kitty escaped and joined Cyclops, Phoenix, and Nightcrawler in an attempt to rescue Logan and the others. It was Kitty, using her newly emerged mutant powers to walk through walls, who freed Logan from the cage that he was imprisoned (Uncanny X-Men #130).

The trapped X-Men regained their freedom, and Phoenix defeated the queen in psychic combat. shortly afterward, the X-Men mounted an assault on the Hellfire Club's mansion in Manhattan. Nightcrawler and Logan sneaked in the underground through the sewers. Upon entering the mansion, Logan was attacked by the Inner Circle's White Bishop, Donald Pierce. Logan slashed off Pierce's left arm, discovering to his amazement that it was robotic. Pierce was a cyorg, part man and part machine. "Yeah, I know all about cyborgs," Logan said, adding enigmatically, "I almost became one myself."

Logan did not fare so well against the Inner Circle's Black Bishop, Harry Leland, who had the mutant power to increase the mass of anything temporarily. Leland made Logan so heavy that he sank though the floor back into the sewers. When he got back inside the mansion, he hid in the basement, holding onto the ceiling, while costumed Hellfire Club mercenaries searched for him. Then he leapt on them, slashing out with his claws, taking pleasure in wreaking such havok. Two mercenaries fell, bleeding from the wounds his claws inflicted, but then the other, by the name of Cole, shot Logan point blank.

Cole thought Logan was dead, but then Logan was back on his feet, slicing away. Cole's gunburst had nearly cut Logan in two. His healing factor had kept him going, but he still needed time to recover completely. Wearing an unnerving smile, Logan said, "Hey, bud. I know what you're thinking'. 'He's hurt, an' he's five meters away from me, an' I got a full clip of ammo in my rifle. Question is, can I kill Wolverine before he can reach me an' cut me into shish-kebab with those freaky claws of his?' "

The mercenary was visibly shaking now and dropped his gun. Logan reflected in his thoughts, "I've mellowed some since joinin' the X-Men. In the old days, I wouldn't have given this punk the choice."

Logan left behind the bodies of 3 Hellfire Club mercenaries. But his three victims were not dead, and Logan would see them again in the very near future.

By now the Inner Circle had taken the other X-Men prisoner. Worse, the X-Men's old foe, Mastermind, needed to prove he was worthy of joining the Inner Circle.

Mastermind had been psychically brainwashing Phoenix over some time, and so decided to complete the brainwwashing, turning her into the Innet Circle's new decadent Black Queen.

Unstoppable, Logan fought his way through the mansion. finally, he crashed through the door to the study of the Inner Circle leader Sebastian Shaw. Chaos ensued. The captive X-Men broke free, and Phoenix regained her self-control. wolverine leapt at Leland, who used his mutant power on him again, making him so heavy that when Logan landed on him, they both crashed right through the floor.

The X-Men escaped the mansion, only to face a danger not just to them but to the whole universe. Mastermind's tampering with Phoenix's psyche had unforseen results, transforming her into Dark Phoenix, an insane creature of seemingly limitless power, devoted utterly to destruction. She easily overpowered them in battle and then went off to wreak further havok.

The X-Men caught up with her outside the home of Jean Grey's parents, and this time they were prepared. They managed to fasten on her head a scrambler device constructed by Beast that would limit her powers. Even so, she was more than a match for the entire team.

Desperately, Logan pushed her into a nearby body of water. he believed her to be the real Jean Grey - the woman he was once in love with and still cared for deeply. even so, he planned to kill her. "Ev'ryone else is holdin' back," logan thought. "They keep thinkin' Dark Phoenix as Jeannie. They're tryin' ta capture her without hurtin' her any more than they have to. But that won't work." He made a decision. "I got no choice. I gotta end this - now! Permanently." He unsheathed his claws and looked grimly at the struggling Phoenix. "Forgive me, darlin'," he told her.

Then, abruptly, she looked up at him in tears, having reverted back to Phoenix. "D-do it, Wolverine!" she pleaded with him. Logan looked stunned. His old feelings for Jean overwhelmed him, and he hesitated.

By then it was too late. Seeing an opening, the Dark Phoenix personality took hold once more and blasted Logan away. "for an instant Jean was back," he told himself. "I couldn't." Logan will find himself in this same situation soon, when he is forced to help kill Mariko - at her request.

It was Professor X, the most powerful telepath on the planet, who put an end to the threat by helping the normal personality of Phoenix take control once more. It seemed as if the menace of Dark Phoenix was over permanently. But then, the X-Men were all transported aboard the Shi'ar flagship of their ally, Lilandra, who was now empress.

Empress Lilandra decreed that the being thay all still believed to be Jean Grey was too dangerous to live (Uncanny X-Men #137). As a result, the X-Men decided to participate in a trial by combat againsst members of Lilandra's Imperial Guard to decide Phoenix's fate.

The night before the battle, Logan reflected in solitude on what the next day might bring. "I ain't scared of dyin'," he told himself. "Never have been. It'll happen to me one day, whether I want it to or not, so why waste time worryin' about it."

Then he thought about Phoenix. He saw a similarity between himself and the side of his personality that took him over in his beserker rages, and Phoenix and her Dark Phoenix persona. Perhaps this realization increased his sympathy for her. "Nobody understands Jeannie like I do - that she's become two seperate entities; Jean Grey an' Phoenix. But to Logan's mind, there was no link between those two personalities as there was between his. "Jean ain't a killer. She can't be held responsible for Phoenix's actions." He settled into a traditional Japanese position for meditation. "But if push comes ta shove - if I have to make a choice - I stand with Jeannie all the way!"

The trial by combat took place on the blue area of Earth's moon, a section with it's own atmosphere. During the combat, Logan found himself inside the home of Uatu the watcher, the powerful alien who has observed the entire history of life on Earth into the present. Unable to comprehend the literally unearthly sights within the house, Logan felt his fragile sanity beginning to slip away. Uatu finally intervened, hurling Logan from his domicile.

At the climax of the battle, Phoenix reverted to Dark Phoenix again. Now Logan believed there was no hope of saving the woman he cared for. The desperation and heartbreak Logan felt was heard in his voice. "Don't you guys see? We're not facin' Jeannie anymore, but Phoenix! Like it or not, it's us - an' maybe all humanity - or her. I... loved that woman, Petey. Because o' that love, I might hesitate. It happened before." Aided by the moon's low gravity, he threw Colossus at the raging Dark Phoenix. But Colossus, too, could not bring himself to kill his friend. He pulled his punch, leaving her alive.

Finaly, Phoenix once again seized control long enough to activate a weapon that disintegrated Phoenix's human form, putting an end at last to the menace of Dark Phoenix.

Emotionally wounded by what he believed was the death of the woman he loved, Scott Summers took a leave of absence from the X-Men. It will be years before Logan and the other X-Men learn that the Phoenix was not, in fact, Jean Grey.

Sobered by the loss, Logan takes to wearing the brown-and-orange costume (Uncanny X-Men #139) that he once wore to battle Zaitsev, perhaps to serve as a reminder that his role as super-hero is no less dangerous than his previous one as government agent.

Nightcrawler asked "Wolverine, I've been meaning to ask you: why the new costume?"

"Why not?" Logan responded. He was not interested in discussing it. Logan will wear this alternate costume for years before returning to his more familiar yellow-and-blue one.

The day that Scott left, Kitty Pryde arrived to begin her training at Xavier's school (Uncanny X-Men #138). Logan has a fondness for children, and he remembered how Kitty saved him form the Hellfire Club. so it was that son after her arrival, seeing her stand apart from the others, he decided to so something about it. "She's shy," he thought, looking at her. "She doesn't know where she stands yet - apart from the X-men or a part of it. That's a real lonely place to be." And Logan knew all too well what it was like to be alone.

"Hey pun'kin," he called. "What're you doin' over there... when ya should be over here, with us? You're an X-Man, ain'tcha?"

Kitty was confused, but utterly delighted, and that was the beginning of what might have seemed the unlikeliest of friendships.