BIOGRAPHY - Page 10
Though free of Apocalypse, the experience left Cyclops deeply changed. While he still was a fantastic strategist and self-confident leader, he became more ruthless and started to doubt both himself and his relationship with his wife Jean. Both he and Jean became active members of the X-Men again but the marriage started undergoing a strain as Jean felt that Scott was keeping secrets and acting cold toward her. [New X-Men (1st series) #114, 118]
Also adding strain to Scott's life was the recent mutant genocide that occurred on Genosha, wherein a battalion of Wild Sentinels unleashed by the villainous telepath Cassandra Nova laid waste to the entire island, killing the 16 million mutants who lived there. One of the only survivors was Emma Frost, the former White Queen of the Hellfire Club. Emma survived purely due to the sudden activation of her previously unknown secondary mutation of turning into solid diamond. Afterward, the understandably traumatized Emma Frost came to live at the Xavier School. [New X-Men (1st series) #114-116]
While investigating the murder of X-Corporation Hong Kong member, Risque, the X-Men came across a trail of illegal mutant organ trade between U-Men leader, John Sublime, and the Chinese government. Their latest victim was to be Xorn, a Chinese mutant with a tiny sun in his head, who should have been a new spiritual leader, but was instead kept as a prisoner of the Chinese government for fifty years. Finally free, Xorn wanted to commit suicide by collapsing the sun in his head into a black hole—an act that would have destroyed the Earth—but Cyclops managed to talk him out of it, making him see new possibilities and eventually befriending him. During that adventure, Cyclops also grew closer to his new teammate, Emma Frost. She propositioned him sexually in Hong Kong and, although Scott turned her down, they did talk through the night about his problems in a way he hadn't been able to talk with Jean. [New X-Men Annual 2001, New X-Men (1st series) #139] 
Some time later, when the X-Men were in need of a healer, Cyclops recruited Xorn for the team. Emma, meanwhile, proved to be an asset to the team. When Cassandra Nova infiltrated the school and staged a deadly, multi-pronged attack on all who resided there, it was Emma who finally subdued her by transferring the sadistic telepath's consciousness into an inescapable alien container. Emma's brief psychic contact with Cassandra would have ramifications for her much later on, however. [New X-Men (1st series) #122-126]
Later, Scott confided in Emma—the X-Men’s self-appointed sex therapist—that he was still unsettled by his time as Apocalypse. 
Afraid of the darkness within himself, he considered his relationship with Jean to be only a façade and was unsure how to honestly talk about his feelings. His wife apparently reverting back into the Phoenix didn’t help much in that regard. With Jean away, traveling around the world and visiting the diverse X-Corporation headquarters, Emma agreed to serve as Scott's therapist, which grew into an odd psychic affair. [New X-Men (1st series) #128, 131, 136]
When Jean returned from her world tour, she caught the two of them during one of their sessions and things turned ugly, as she confronted Emma telepathically. Scott finally interrupted this incredibly one-sided psychic confrontation by showing Jean that nothing physical had happened between he and Emma and then left the mansion, deciding to quit the X-Men. [New X-Men (1st series) #139]
While Scott was busy getting drunk and pitying himself at the Hellfire Club, which was now a mutant strip club, Wolverine found him and bought him several more rounds. With Scott fully inebriated, Logan drafted him into helping he and Fantomex infiltrate the Weapon Plus complex to learn the secrets of Wolverine's past. In the process, after learning about Weapon Plus's horrifying plans for mutants, Cyclops and an injured Fantomex returned to Earth, while Wolverine was left behind. [New X-Men (1st series) #142-145]
Back on Earth, chaos had broken out, as Xorn turned out to really be Magneto, who had once again declared war on humanity. Cyclops and Fantomex rallied several new students of Xavier's behind them and attacked. They were joined by the other X-Men, who'd been saved by Phoenix from several deadly scenarios in which Xorn/Magneto had ensnared them. Cyclops told Emma he had now decided between her and Jean, though he didn't get around to telling Jean the choice. He was furious over "Xorn's" betrayal and brutally attacked Magneto with his optic blasts.
Jean coaxed Magneto into removing his Xorn helmet, allowing Xavier to infiltrate his mind and defeat him. Magneto's final act, as he was beaten, was to kill Jean, who urged Scott to live on without her as she died in his arms. Wolverine immediately decapitated Magneto in response, but it was too late to save the life of the woman both Scott and Logan loved. [New X-Men (1st series) #146-150]
When Xavier shortly thereafter stepped back from his headmaster duties, Emma Frost asked Scott to reopen the school with her. Originally, the guilt-ridden Scott would have rejected both her and the offer. However, influenced by Phoenix, who now dwelled on another plane of existence, Scott changed his mind and said ‘yes’ to both. 
Unfortunately, he now had to face the disapproval of the other X-Men, who were somewhat disgusted by his starting another relationship so soon after his wife’s death. None were quite as angry as Wolverine. Because he carried a torch for Jean while she was alive, he took the brevity of Scott’s grieving period more personally than others. He physically attacked him in bed one morning because of how quickly he started sleeping with Emma Frost. [New X-Men (1st series) #151, 154-156, Astonishing X-Men (3rd series) #1]