BIOGRAPHY - Page 12
Around this time, the X-Men experienced a shake-up when the existence of a series of prophetic diaries written by the mutant Destiny was uncovered, prompting Storm to gather a special team from within the X-Men's ranks to aid her in tracking down and securing these 
potentially dangerous volumes. The knowledge in these books was considered so hazardous that even Professor Xavier himself was not above reproach in the matter, and Storm's team basically planned to leave in the middle of the night without a word, to keep the mission a secret. Ororo asked Logan to remain behind at the mansion, acting as their connection to the rest of the X-Men. [X-Men (2nd series) #109] Their departure left the X-Men severely undermanned, though, and at the worst of times -- Magneto had finally taken full control over Genosha, and was planning to lead an army of mutants against the rest of the world. With Professor X captured by the Master of Magnetism and Jean Grey working to gather a band of interim X-Men to help, Wolverine and the newly-reborn Cyclops were the only remaining X-Men available to infiltrate Genosha and try to stop Magneto from within his borders. During the time they spent together, Logan noticed some changes in Scott's personality following his time bonded to Apocalypse, and tried to get him to open up about it, but to little avail. Miraculously, their efforts proved successful and Wolverine, going one step further than his teammates, assaulted the beaten Magneto with his claws and tore through his chest and spine. Magneto was left crippled and barely hanging on to his life, in no condition to carry out his threats against humanity. [Eve of Destruction crossover]
Logan's problems with Weapon X soon began again when Sabretooth went rogue from the organization, stealing their files on mutants around the world and access to the Program's teleportation technology and other instruments. He planned on selling the mutant files off to the highest bidder and make a tidy profit... but first came his long-awaited final revenge on Wolverine. First, his hired agents Deathstrike and Omega Red attacked Logan's closest friends, nearly killing Nightcrawler and the Hudsons, putting Yukio in the hospital, paralyzed for the rest of her life, and finally kidnapping his daughter Amiko. Next, he commandeered a prototype cannon's command codes from the Program and used it to block Wolverine's mutant abilities with a satellite beam, leaving him powerless. Wolverine tracked his trio of nemeses to Las Vegas but, despite the back-up of one of Guardian's power suits, fell rather quickly before a combined beating of Omega Red and Lady Deathstrike. After dragging Logan before Sabretooth, however, the two villains were cut out of the final dealings when Creed teleported himself, Logan and Amiko right out from under their noses, to do battle with each other in the remains of the original Weapon X compound in Canada. Creed even dangled the "Logan Files" in front of Wolverine, the supposed copy of all his original memories right there for the taking, before revealing the truth: Logan's own healing factor was responsible for much of his memory gaps, "scabbing" over his more traumatic memories to keep him from feeling too much pain. 
Creed's dealings caught up with him, though, as the Weapon X Program regained control of their power suppression cannon and gave Sabretooth a taste of the same medicine he gave Wolverine. Suffering from the injuries he had sustained fighting Logan, Victor was forced to teleport himself to safety without finishing the job when the Program's soldiers tracked them down. Logan did not fare much better, and was clinically dead for 23 minutes before his powers finally kicked back in and restored him to life. Surprisingly enough, Amiko was returned to him alive and well by the Director of Weapon X, in regards "from one father to another." [Wolverine (2nd series) #173-175]
After 16 million mutants were wiped out on Genosha (including Magneto), cutting the worldwide population almost in half, Professor Xavier took a bold step and publicly outed himself and the school as part of the X-Men. [New X-Men (1st series) #116] This led to Xavier's School for Gifted Youngsters reopening to over 100 students, and the current X-Men team adopting a full-time role as educators to the next generation. Meanwhile a second team of X-Men was activated at that time, operating out of both the school and Worthington Industries in New York City so that they could continue functioning as the "mutant strike force" the X-Men had generally operated as in the past. Wolverine made himself available to both these groups -- primarily operating out of the mansion as an instructor, yet on-call for the "away team" whenever their team leader Nightcrawler requested his help. After Kurt stepped aside due to personal issues and ceded leadership to Archangel, though, Logan stopped working with the field team as often, due to the longstanding bad blood present between him and Warren. Still, it seems leadership had a positive effect of Archangel, and he eventually humbled himself and apologized to Wolverine directly for the snap judgments he made about Logan when they first met. [Uncanny X-Men (1st series) #440]
Working with these two teams brought Logan into combat with the Mummundrai called Cassandra Nova and anti-mutant religious fanatics such as the Supreme Pontiff and his agents Mister Clean and the Church of Humanity. Logan did solo missions as well, such as when he rescued a young mutant girl named Angel from the U-Men, fanatical harvesters of mutant organs. [New X-Men (1st series) #118] 
He retrieved another mutant girl, Dust, from Afghanistan, running into the mystery man known as Fantomex in the process, who was also known as Weapon XIII and possessed a greater knowledge about Wolverine's past than Logan did himself. [New X-Men (1st series) #133] In addition, Logan also personally dealt with more pedestrian threats, like corruption in the Vatican and overzealous mobsters in New York City. [Wolverine (2nd series) #177-178, 182-185] Also, when Storm was injured while her splinter faction of X-Men were repelling an alien invasion, Logan made time to visit Ororo and help her with her rehabilitation. While visiting, he also got involved in her team's conflict with Reverend Stryker and Lady Deathstrike. [X-Treme X-Men (1st series) #20-30]
Around this time, Logan learned about a clone made clandestinely from his own DNA. Dr. Sarah Kinney from the criminal science organization known as the Facility sent Logan a letter informing him about a teenaged girl named X-23, cultivated from genetic samples stolen from the Weapon X Program, and raised as the ultimate killing machine. The letter was to warn Wolverine that Sarah planned to rescue X-23 from the Facility, but she wasn’t sure she would be successful. Logan tracked down the Facility, but it was too late – Kinney was dead, the lab was shut down, and X-23 was missing.
A few months later, however, X-23 found him. X-23, who Dr. Kinney named Laura, wanted to kill herself and Weapon X, because they were nothing but weapons too dangerous to survive. She actually overpowered Logan during their confrontation, but he refused to let her kill herself. Wolverine told Laura what happened to her wasn’t her fault, and she had the opportunity to choose her own life now. They spent time together getting to know each other that evening, but SHIELD arrived looking for X-23, and she ultimately disappeared before Logan could convince her to stay with him at the X-Mansion. [X-23: Target X #6]
Though the X-Men managed to win most of their battles, tragedy still managed to find them. The Church of Humanity crucified a group of mutants on the mansion's front lawn, including Jubilee. Wolverine sat by her bedside until Archangel's healing blood miraculously restored her from the brink of death. [Uncanny X-Men (1st series) #423-424] The new students at the school were anything but sanguine as well, and a riot at the institute left several students dead and the teaching staff in disarray. Wolverine chose to step out for a few days after being contacted by Fantomex -- 
in exchange for helping Weapon XIII break into the Weapon Plus Program's hidden laboratory base in England, Fantomex would aid Logan in uncovering information there about the Weapon X Program and his own history. Upon infiltrating the elastic temporal properties of "The World," however, Wolverine (along with Cyclops and Fantomex) learned that agents of AIM had preceded them and accidentally allowed the latest super-soldier to escape -- Weapon XV, born of human flesh and Sentinel nanotechnology. Their battle with the program's newest creation led to a space station maintained by Weapon Plus, and full access to the history of the program, dating back to World War II. Logan uncovered a great deal about the program, its earlier successes such as Captain America and Nuke, and his own history as "James Logan." [New X-Men (1st series) #142-145]
Events took an urgent turn when Logan uncovered information about an informant inside the Institute, working alongside the Weapon Plus Program. As Cyclops and Fantomex barely got to safety in a stolen shuttlecraft, Wolverine stayed behind to detonate a series of explosive charges around the station and fight Weapon XV until they both died in the resulting fireball. But they didn't -- instead, Logan and his fallen opponent were drawn towards a nearby rock in space. By the time Jean Grey arrived in the X-Wing to rescue him, Wolverine had recognized the rock as a fragment of Asteroid M, left there as a trap for them. Indeed, a set of booby-traps destroyed the X-Wing and left Jean and Logan trapped on the asteroid, hurtling into the sun. They slowly began to be cooked alive, as the temperature continued to rise. Jean inexplicably found herself unable to access the power of the Phoenix to save them, and Logan took it upon himself to mercy-kill her with his claws instead of letting her burn to death.
Luckily for them both, this act released the Phoenix within Jean, and she self-resurrected with enough power to save them both and bring them back to Earth, alive and relatively well. Along with the rest of the X-Men, they confronted the traitor Xorn in New York City. During the battle, Jean confronted Xorn who had revealed himself as Magneto. Crazed and defeated, Xorn unleashed a localized electromagnetic pulse that caused Jean to have a massive stroke. Jean Grey died before everyone's eyes, for good this time. Wolverine went berserk and decapitated her killer before anyone could think of stopping him. [New X-Men (1st series) #146-150]