- The weak will be culled from within our own forces to create a true elite race and sit our sight beyond. You once asked me how I felt about humanity's demise, Azazel. It feels invigorating to be beyond that albatross.
- -- Weapon Omega (Logan) src
Prior to Apocalypse taking over North America and decimating much of the rest of the world, Logan was traveling through Japan. He rescued young Mariko Yashida from members of the Yakuza. This angered her half brother, the Silver Samurai, leading to a clash between the two men. Logan won the fight, but spared the Silver Samurai's life. Logan later had a brief relationship with Mariko, and unknown to him, had a daughter named Kirika. Their romance ended due to some unknown conflict with her father Shingen.
When Magneto was recruiting mutants to be part of his X-Men, he recruited Logan to his cause, who took the name Weapon X. Although his feral nature made him a deadly fighter, Magneto had Jean Grey use her mental powers to calm his rages, and the two formed a strong bond, which eventually bloomed into romance. When Apocalypse made his first strike on humanity, he targeted Cape Citadel in order to use its nuclear weapons to slaughter mankind. Weapon X joined the X-Men in battling against Apocalypse's Horsemen. During the battle he faced Sabretooth and easily bested him in battle. Sabertooth was eventually abandoned by Apocalypse, causing him to join up with the X-Men, where he and Weapon X became allies. During an attack on one of Apocalypse's facilities, the two of them found young Clarice Ferguson and rescued her, adding her to the X-Men's ranks.
Weapon X became at odds with Magneto when Jean Grey was captured by Sinister for experimentation. Magneto refused to send the X-Men into Apocalypse's citadel to rescue her. Unwilling to accept that, Weapon X went after her alone. In a battle against Cyclops, Logan lost his left hand, but not before he cut out one of the Prelate's eyes. Logan capped the stump of his lost hand with a metal band. After liberating Jean, Weapon X and Jean left the X-Men, and continued to fight Apocalypse by themselves.
Weapon X and Jean Grey
Sometime later, the two lovers became affiliated with the Human High Council, being the only mutants granted amnesty and given immunity from even the Sentinels. They were given data from Sinister regarding Apocalypse's sea-wall defence perimeter and handed it over to the Council so that they might plan a Sentinel evacuation of the remaining humans in North America. With the data confirmed, Weapon X and Jean were dispatched to sabotage one of the primary sea-wall towers to allow the Sentinels to get through. They clashed with Havok, but managed to defeat him, fusing his body to a Sentinel's gauntlet through a teleporter. Their mission was a complete success and they returned to Europe. There, the Human High Council began to consider launching a full out nuclear strike on Apocalypse, when their meeting was interrupted by Apocalypse's agent Magma. Weapon X killed Magma and her attack on the council convinced the members to go ahead with the nuclear strike. This formed a wedge between Jean and Logan, as Jean believed that there must be some other alternative, while Weapon X believed that nuking Apocalypse was the only way to save the world.
When the Sentinel evacuation was successfully underway, Jean helped with registering all the humans refugees. Fearing Jean was leaving him, Logan tracked her there, where the two of them spotted Apocalypse's agents, Box and Copycat, trying to smuggle their way into Europe. Weapon X and Jean killed the two, unaware that they were merely a distraction to allow cyborg Donald Pierce and his Reavers to sneak into the country. Logan and Jean argued over the council's plot to nuke America and Logan, unable to convince Jean to accept the Council's decision, told her that she should do whatever she needed to do. Back in London, Weapon X met with Mariko, now a member of the council, and she expressed her concerns about her fellow council member Brian Braddock who had been acting very strangely. Before they could discuss things further, the primary air ship was attacked by Pierce and his minions. Weapon X managed to fight them off, but not before they destroyed the primary navigation system of the ship. In the battle's aftermath, Logan sensed that Jean was leaving, and he rushed to the airfield where her plane was taking off. Jumping on board, he gave her one last kiss and let her go.
Needing a new means to get their ships to America, the council sent Weapon X to convince the mutant teleporter named Gateway to help. Going to his hideaway on Wundagore Mountain with his old friend Carol Danvers, Weapon X clashed with the Reavers again. In the battle, Logan destroyed the Reavers sent to kill Gateway, but Carol sacrificed her life to save them. Gateway agreed to go with Logan and at least give the council a chance to convince him to help. Weapon X and Emma Frost managed to win over Gateway, but while mobilizing their fleet they were attacked by the Reavers once more. Weapon X was shocked to find that Pierce had converted Carol into one of his cyborgs. In the course of the battle, Brian Braddock was revealed as a traitor and slain by Pierce himself. However, in the final battle, Pierce was betrayed by Carol, and he killed her as well. This infuriated Weapon X. With his good arm wounded and useless, Pierce mocked Logan for being unable to fight back. However, Logan had a lethal surprise for Pierce: he revealed that he still had claws retracted in his arm after his hand was severed, and impaled Pierce with them. With Pierce's threat ended, Weapon X accompanied the airships to the United States.
Arriving there, Weapon X parachuted down to Manhattan to search for Jean Grey so that he could spend his final moments with her. He arrived just in time to see Jean seemingly being slain by Havok. While battling his brother Cyclops, Havok failed to notice Weapon X sneaking up behind him, and Logan killed him. With the nuclear weapons raining down on them, Logan waited for the coming doom while cradling Jean's dead body in his arms. However, they were saved when Jean, who unknown to them, was still alive and tapped into the Phoenix Force and saved them all.
Return to the X-Men
Following the fall of Apocalypse, Magneto and the X-Men began rebuilding the United States, while Logan lived in relative seclusion in Canada, hunting down any minions of Apocalypse who had fled there. Unknown to Logan, Jean was still alive and had been taken away by Sinister. As Magneto was believed to be the one that saved the world, he was made head of the Department of Mutant Affairs and in charge of rounding up Apocalypse's minions. Sinister used the truth to blackmail Magneto into keeping away from him.
Eventually, Magneto found Kirika in one of Sinister's old labs, and freed her. Unsure of her origins, she joined the X-Men. After Magneto bonded her bones and claws with Adamantium, he sent her to Canada to convince Logan to come back to the X-Men. At first, Logan was against meeting with the young girl or the prospect of going back to work with Magneto. However, after the two fought and killed Northstar and Aurora, he agreed to return to the X-Men to help hunt down Sinister and other war criminals that had been part of Apocalypse's regime.
Weapon X's return to the X-Men was mostly welcome, with the exception of the Silver Samurai, who had joined the group in Logan's absence. The two almost came to blows until Kirika stepped in to break up the fight. Logan then joined the team in traveling to Washington, D.C. to stop the rampage of Amazon, Cannonball and Icarus, former members of Apocalypse's Elite Mutant Force. Logan helped his fellow X-Men fight off their attack. However it was merely a diversion allowing their sister Paige to capture Rogue and her son Charles as part of a revenge scheme for the X-Men abandoning her during Apocalypse's reign. Logan and the others slew the Guthrie family, but not before Paige revealed that Magneto had been letting Sinister run free. Magneto confessed that he had been keeping Sinister's secret all along.
The fact that Jean's survival had been kept from him infuriated Logan, but he refrained from killing Magneto. He called on Magneto to right his wrongs by helping bring Sinister in. Logan destroyed Magneto's helmet, telling him that he had to do it without hiding behind a mask. Taking a scent off Paige's corpse, Logan led the X-Men to Sinister's hideout on Staten Island. There they clashed with Sinister's Sinister Six, which included Jean among their number. In the final battle, Weapon X convinced Jean to shake off Sinister's mental conditioning, and she turned her powers against Sinister. Ultimately, Weapon X and Kirika killed Sinister. In the battle's aftermath, Psylocke revealed that Kirika was Logan's daughter through Mariko. Kirika parted ways with her father to return to Japan, while Logan remained with the X-Men. With Magneto voluntarily turning himself over to the authorities for his deceptions, Logan and Jean kept the X-Men together, working as joint leaders to ensure that human/mutant peace endures.
Heir of Apocalypse
For some time things were good until a spaceship landed in the middle of Manhattan. Logan and a squad of X-Men were sent to kill whoever was inside it but never returned so they were presumed dead for ten years.
However, the spaceship belonged to the Celestials who had come to judge the planet. Logan offered himself to the Celestials to prevent the planet's judgment and was further augmented by the Celestial technology, yet while he had ascended in form and power, his mind had become so twisted to the point of assembling a deadly group of genetically modified warriors known as the Black Legion. Logan sent them to kill Charles Lehnsherr, the infant son of Magneto and Rogue and started a genetic culling that killed billions of people including the parents and friends of his wife Jean Grey. He also captured his teammate Storm and renamed her as Orordius after using the Celestial technology on her to enslave and transform her into a blind seer made of living stone. He also captured Gateway and locked him in a prison named Sky. When the X-Men and X-Force from Earth-616 came to save Gateway so he could help them, Logan killed his daughter Kirika and revealed himself.
The team was shocked to see that he was the heir of Apocalypse. His counterpart was also shocked to see Kirika, the daughter he never had dead in his arm, so he went feral and attacked his evil counterpart along with the other members of X-Force. Weapon X was not interested in fighting them but did when he realized they would not leave only for his wife tjjjo stop them. He asked her to listen to him for a while but she questioned his actions and what he had done to their world. He told her he had no choice and if evolution didn't move forward the Celestials would have destroyed the planet if they saw it as a failure so he ascended to save everything and to save her. She questioned him about what he had become he answered that he served a natural cosmic force for evaluation, there was no right and wrong in what he did and he cleared the dead branches to make room for a healthier stock. After hearing this Jean declared that he was not the man she loved, he told her he took a few steps above him, the Celestials didn't intend for humanity to reach the final stage, humanity had to go, the culling was almost over and there was no undoing this, but with her power, their world could be reborn and she could save her friends, stop the war and they could be together if she helped him rebuild.
Jean was tempted by this offer, but refused and attacked him while telling him she would never build a life atop a graveyard of his own making. He responded she would change her mind before he hit her unconscious with one strike. He teleported with her to somewhere else intending to turn her into the Horseman of Death, but his efforts were prevented by the X-Force. His counterpart wanted to take Jean back with him to their world - this made him enraged so he fought and defeated his former teammate to get to her and implant the Death Seed in her. He was seen approaching Jean with the Death Seed in his hand while she pushed the X-Force through a portal to their world.
She managed to escape him, and Weapon Omega proceeded to launch his plans to destroy the humans' final city. The human resistance revealed a secret plan which involved creating cloned bodies of the Scarlet Witch and having a telepath control one of the bodies to use her ability to alter reality and wipe out mutants. The plan failed and Weapon Omega managed to kill Rogue and Magneto while Jean and Sabretooth were depowered. He managed to destroy the last human city and it was revealed that he had been bringing back deceased Alpha mutants like Scott Summers using energies siphoned from the celestial life seed.
After discovering the resurrected Penance he ordered his servants Azazel, Cyclops and Colossus to bring her into the fold. She initially refused however and undid Colossus' brainwashing causing him to abandon Weapon Omega and serve Penance. A fight broke out but Azazel agreed to leave. He returned with Weapon Omega who demanded that Penance knelled before him which she did. Unbeknownst to Weapon Omega however Penance was also making deals with the Human Resistance.
After being alerted that Jean Grey was hiding out in the city, Weapon Omega resolved to hunt his wife down himself and vowed that if her humanity could not be cured, he would kill her himself. 
He found her in the sewers beneath the city, fighting off the dregs of the society. Before he could do anything, Sabretooth got to them and began to fight him, whilst Jean slipped away. She met with her allies, who gave her a small pill that Sugar Man had created. If ingested by Weapon Omega, the bean would strip him of the Celestial influence. Weapon Omega easily beat Sabretooth and began to hunt Jean down. She took the pill and decided to stay behind, whilst the others fled. Weapon Omega captured her and had McCoy run extensive tests on her, at which point he learned she was now irrevocably human. Going to visit her one last time, Weapon Omega did not notice when she slipped the pill into her mouth. As they kissed for one final time, she slipped the pill from her mouth to his, where its effects immediately began to show. 
Weapon Omega stabbed her in response, but it was too late. The death energies tore out of him and were absorbed by Jean as the next host. Thanks to her history with the Phoenix Force, though, Jean was strong enough to reject the power of the Death Seed and displaced it. After everything died down, Weapon Omega emerged from the rubble as Logan once again, his mind now clear of the corrupting force of the Death Seed. Unknown to him or Jean, however, the energies of the seed had in fact been contained by Bolivar Trask in a giant machine under the Nevada Desert.
In the aftermath, Logan began hunting down all the mutants who worked for him under his regime. It was in New York, where he had tracked and killed Cyclops, that Logan was in turn found by Jean. Having spent a long time trying to find him, she asked him to come home. He declined though, as he was still feeling guilty over his actions when he became Weapon Omega. He told Jean there would never be peace for him in this new world and now released her from any obligation she had to him. With Emplate on the loose in Brazil, his sights were set on his next target.
Weapon X is an Alpha-Class Mutant, with a powerful healing ability strong enough to extend his lifespan. Weapon X also possesses extremely acute senses, making him an expert tracker. He also has claws that extend from his wrist. Lacing his entire skeletal structure is a virtually indestructible metal known as Adamantium.
Since becoming Weapon Omega, his power has vastly increased it can be assumed that is at the same levels as that of Apocalypse.
- Logan/Weapon X had no known relation to the Wolverine who used the name in this reality and was Holocaust's minion.
- Unlike his predecessor, Weapon Omega does not appoint Horsemen, instead, he bestows the title of Minister on his most trusted servants. Azazel is the Minister of Death, Cyclops is the Minister of Famine, Havok is the Minister of War and Emplate is the Minister of Pestilence. Each Minister has an area of control and special troops.
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