BIOGRAPHY - Page 11
With his resolve renewed thanks to Jean's posthumous psychic nudge, Cyclops re-formed the X-Men with the goal of rehabilitating both their reputation and the reputation of mutantkind as a whole. He and Emma hand-picked a team that included Beast, Wolverine and Kitty Pryde to be public superheroes whose primary goal was to astonish the world. [Astonishing X-Men (3rd series) #1]
As co-headmaster of the Xavier Institute, Scott also had to deal with the administrative responsibilities of running the school (and all of the other teams of X-Men). He and Emma divided the students up into small squads, each of which had an experienced X-Man as a mentor. Cyclops led a squad he called the Corsairs and, as headmaster, dealt with inter-squad squabbles as well as conflicts his students had with the outside world. [X-Men (2nd series) #157, New X-Men: Academy X #1-6]
Scott’s "Astonishing" X-Men team soon had its chance to shine. When an alien named Ord from the Breakworld invaded an upscale gala and took its attendees hostage, Cyclops and his team came to the rescue. They took a beating but, with the help of Kitty's dragon Lockheed, managed to defeat Ord and save the hostages. 
Immediately after this battle, they learned that a scientist named Kavita Rao had developed a "cure" for the X-gene that she intended to make accessible to any mutant who wanted it. Curiously enough, Cyclops discovered that Ord and his associates were brandishing advanced SHIELD weaponry during their attack. Fearing there was some connection, Cyclops confronted Nick Fury and demanded information, but found him noncompliant and evasive, possibly due to his lingering resentment toward mutants because of what Magneto had done to New York City.
Meanwhile, Beast identified the DNA of the mutant used to help refine Rao’s Cure — and recognized it as the DNA of someone they intimately knew. The X-Men infiltrated Rao’s laboratory, where they were ambushed by the facility’s guards and Ord. Meanwhile, while most of the X-Men were subdued, Kitty infiltrated the rest of the facility and was able to rescue the mutant test subject being held in captivity: Colossus, whom the X-Men believed to be dead. Kitty re-emerged with Colossus, who beat Ord mercilessly, and the X-Men subdued him before he could escape back to the Breakworld. However, to Cyclops’ chagrin, Fury and Agent Brand of SWORD granted Ord diplomatic immunity. When he pressed them on this arrangement, Cyclops learned that Ord’s home planet had declared war on Earth due to a vision one of its precogs had involving a mutant destroying the Breakworld. As a compromise with the Breakworld, SWORD agreed to let them develop and distribute the Cure on Earth in order to neutralize its mutant threat. Cyclops was not pleased with this arrangement, which he considered a betrayal against his people. [Astonishing X-Men (3rd series) #1-6]
Even though Jean had died, Scott still had feelings for her, which created a chronic source of tension with Emma—especially when the Phoenix continued pestering him. He received a visit one night from a weakened Phoenix Force, which, after waking him and the X-Men, moved on to Jean's grave, where it brought her back from the dead. Scott struggled to resist the lure of the Phoenix and had Beast build a "containment egg" that could subdue its immense power. 
When the Phoenix overtook Scott and used his optic blasts to power itself, Emma invited the Force into herself, at which point Cyclops threw both her and himself into the containment egg. While inside, they shared energy and further empowered the Phoenix Force. However, the egg broke and the Phoenix Force escaped and made its way back to its original host, Jean Grey. Fearing she would go Dark Phoenix, the X-Men telepathically reminded her how loved she was and convinced her to stand down. Jean and the Phoenix returned to the White Hot Room, leaving Scott with Emma, both of them free of the Phoenix—for the time being. [X-Men: Phoenix – Endsong #1-5]
Meanwhile, the Danger Room, which apparently had been sentient since Professor X upgraded it with Shi'ar technology and artificial intelligence so many years before, finally managed to break free, give itself a human form and retaliate against its oldest enemies: the X-Men. After Cyclops and his X-Men fell to "Danger" in battle, she traveled to Genosha to kill her primary nemesis, Professor X—the man who had enslaved her and ignored her telepathic pleas for help. 
Despite Emma mysteriously abandoning her team during the climactic battle that ensued, the X-Men managed to defeat Danger this time and save Professor X. However, they were disappointed to learn that he had known the Danger Room had been a sentient being for years, and that instead of helping it after its awakening, kept it as his prisoner for the greater good of training the X-Men. When Xavier claimed doing so was necessary to protect his people, the angered X-Men told him he sounded a little too much like Magneto. [Astonishing X-Men (3rd series) #7-12]
While the X-Men were rife with internal conflict, their allies the Avengers were having some major internal problems of their own. Magneto's daughter, the Scarlet Witch, had gone crazy and killed several Avengers when her reality-warping powers went haywire. The Avengers met with several of their friends, including Cyclops and his team of X-Men, and reluctantly agreed they needed to put Wanda down before her powers destroyed the world. Cyclops accompanied them to confront her in her hiding place on Genosha. However, as they approached her, Wanda transformed all of reality into a mutant-dominated world known as the House of M. In this revised reality, Magneto was king, Quicksilver, Polaris and the Scarlet Witch were mutant royalty, and Cyclops was happily married to Emma Frost. 
However, there existed one flaw in Wanda's restructured world in the form of a little girl named Layla Miller, who not only remembered the way the world used to be, but had the power to make others remember as well. After Layla restored Scott's, Emma's and Logan's memories, they gathered with the rest of the enlightened heroes and launched an assault on the House of M with the hopes of somehow putting their world back to normal.
During the ensuing battle, Magneto learned the truth of their world and that it was actually his son, Quicksilver, who had manipulated Wanda into creating it. Enraged, he murdered Quicksilver, causing Wanda to finally snap. Now believing that mutants caused nothing but problems for the world, Wanda uttered the words "no more mutants" and snapped reality back to its original form—with the major difference of there now being only a handful of powered mutants left. Her reality warp had stripped 99 percent of the world’s mutants of their powers, leaving the mutant race in shambles. 
Most of the students in Cyclops's care no longer had the X-gene, while Polaris, Quicksilver, Magneto and Professor X found themselves among the depowered as well. [House of M crossover]
Because he had been present for both reality warps, Cyclops—along with Emma, Kitty and Wolverine—was one of the rare few on Earth who knew why the mutant race had been devastated on "M-Day." However, they all chose to keep the cause a secret from the world. Scott immediately went into triage mode to salvage what he could of the mutant race. Following a terrorist attack on an X-Corporation office, he shuttered all of the X-Corporations around the world. He also ordered all of the depowered mutant students to leave the school while opening it up as a refuge for all of the world’s remaining mutants. Soon, piloted Sentinels from the Office of National Emergency (O*N*E) arrived to secure the grounds. [House of M (1st series) #8, Decimation: The Day After #1, New X-Men (2nd series) #20, Generation M #1]
Although it quickly became clear that the Sentinels were there to protect the X-Men instead of killing them, Cyclops still confronted Val Cooper and demanded that she make the Sentinels leave. She refused and the X-Men soon began to accept that they would have to live in the shadow of the monstrous robots best known for trying to eradicate them. It wasn’t all for naught, though: when a terrorist group called the Sapien League bent on exterminating the world’s remaining mutants attacked the Xavier School, the O*N*E Sentinels helped the X-Men repel them. Still, the mansion safe haven Cyclops had offered the remaining mutants had become a government-enforced reservation. [X-Men (2nd series) #177-179]
In the midst of the devastation of M-Day, a group of Shi’ar assassins called the Death Commandoes slaughtered all of Scott’s former in-laws in the Grey family in order to prevent the Phoenix from rising again. Only Rachel Grey survived the massacre. The heartbroken Scott wanted to murder the Shi’ar Death Commandoes after subduing them but was convinced to leave them in SHIELD’s custody. [Uncanny X-Men (1st series) #466-468]
Meanwhile, the sanctuary for mutants Cyclops intended to provide proved to be more difficult to manage than he realized. The school was so overloaded with mutant refugees that they had to set up a makeshift tent village for them on the grounds in front of the school. 
The occupants of this camp, who took to calling themselves "the 198," grew irritated at the way the X-Men treated them in contrast to the mutants inside the school. To make matters worse, the X-Men consented to letting the O*N*E insert electronic tracker chips into the 198, but not into the X-Men. This already volatile situation was pushed even further over the edge by a self-hating mutant and psionic manipulator named Johnny Dee, and devolved into a mass exodus and full-scale riot that resulted in the death of Absolon Mercador, one of the 198's spokesmen. This situation showed Cyclops that leading the remnants of the mutant race was going to be even tougher than he imagined. [X-Men: The 198 #1-5]
Back at home, Cyclops’ anger at Emma for abandoning them during the fight against Danger on Genosha continued to simmer, as she still refused to tell him where she had gone. [Astonishing X-Men (3rd series) #13] 
They also disagreed over what to do with the students who were still mutants and were to remain at the school. Cyclops argued they should be kept out of the field and be given the chance to live relatively normal lives as students, but Emma vehemently disagreed, asserting that "normal" was over and they needed to prepare them for the harsh reality they faced in the new, mutant-less world. Cyclops was infuriated when he found out she made the remaining mutant students battle each other to see who would make the cut for a new X-Men training squad. [New X-Men (2nd series) #21-23]
As for the depowered students, Cyclops and Emma loaded them up on a bus and sent them back home. However, to their horror, a group of religious-fundamentalist anti-mutant terrorists called the Purifiers launched a missile at the bus as it was leaving the grounds, killing all 43 depowered students aboard. [New X-Men (2nd series) #23-24]
Later, mere days after the X-Men had buried their dead, the Purifiers led by Reverend William Stryker followed up this attack with an assault on the school. Three more students died during the invasion but the squad of New X-Men Emma had created managed to neutralize the threat. [New X-Men (2nd series) #25-27]