BIOGRAPHY - Page 14
As if anti-mutant hatred were not bad enough on its own, the X-Men's enemies soon concocted ways to make mutants seem even more evil than the public already believed them to be. The recently resurrected Bastion and the Purifiers had obtained a sample of the Legacy Virus and were using it to turn captive mutants into "living bombs" that they detonated at anti-mutant rallies. The first such attack, which the media blamed on a mutant, killed over a thousand attendees at a Friends of Humanity rally. Cyclops ordered X-Force to stop the next attack from happening, but they failed and hundreds more humans died.
On the side, Cyclops continued overseeing Beast's time-travel work, while continually monitoring the timestream for traces of Cable or Bishop. Cyclops refused to admit to Beast why he was having him build seven different time-travel devices or what they were for, though Beast correctly deduced they were intended for X-Force to use so they could find and kill Bishop. When news came that members of the Sapien League had kidnapped three of the X-Men’s former students and intended to detonate them as well, Cyclops sent X-Force to save them, though as their prime directive remained going after Bishop he equipped them with Beast’s time-travel armbands in advance. 
Just as X-Force closed in on the captive Boom-Boom and prepared to save her, Cyclops and Beast caught a glimpse of Cable's signal in the timestream. Cyclops refused to let this opportunity go. Despite Beast and X-Force's cries that they just needed a few more seconds to save Boom-Boom, Cyclops pulled the switch on their time-travel devices, sending all of them to Cable's location in the future—and leaving Boom-Boom to certain death. [X-Force (3rd series) #12-13]
Miraculously, X-Force managed to complete their mission in the future of protecting Cable and the messiah baby (now a teenaged girl named Hope), and returned at the moment they left in order to successfully save Boom-Boom. However, saving her was no guarantee, and the team—especially Wolverine—was understandably angry at Cyclops. When Wolverine attacked Cyke and told him that the responsibility for any of their captive wards' deaths was his fault, Cyclops didn't argue; he accepted full responsibility for the choices he was making. [X-Force (3rd series) #18]
Although Scott's legal maneuvering had kept the X-Men (and mutants in general) out of the Superhuman Registration Act, legal attacks on mutantkind continued. Simon Trask soon unveiled a piece of legislation called Proposition X that would legally prohibit mutants in California from reproducing, riding a wave of public fear after the Cooperstown, Alaska massacre. Understandably, the X-Men were outraged. Amidst this tension, their new base of operations came under attack by the incorporeal Madelyne Pryor and her "Sisterhood." The ambushed X-Men quickly fell to their assailants, but Cyclops got the last laugh when he tricked Maddy into attempting to merge her psychic being with that of an incompatible corpse. He bid farewell to his vengeful ex-wife, who was seemingly destroyed once again. [Uncanny X-Men (1st series) #508-511]
Beast, meanwhile, was through with all of Cyclops's nefarious activities and Emma's secrets, and confronted them both one night in their bedroom while they slept. After he left, Cyclops and Emma finally got to talking and revealed to each other what they had been hiding. For his part, Scott confessed to forming X-Force and sending them on kill-missions, but added that he had done everything with the best interests of the mutant race in mind. Emma's revelations, however, came as a surprise to him: after Norman Osborn had replaced Tony Stark in charge of the SHRA, she had joined his top-secret Cabal of influence peddlers who controlled world events from behind the scenes. But this, she swore, was also done with the best interest of mutants in mind. Revealing their dark secrets to each other actually brought them closer together, but they agreed to never keep secrets from each other ever again. [Uncanny X-Men (1st series) #511, Dark Avengers/Uncanny X-Men: Exodus, Dark X-Men: The Confession #1]
Simon Trask's Prop X campaign finally reached a flash point when he and Humanity Now marched through the streets of San Francisco to demonstrate against mutantkind. A group of counter-protestors, led by Beast, confronted them in the streets and, unsurprisingly, a fight broke out. Worse, it appeared to the general populace that mutants started the fight. Instead of doing some damage control, Cyclops ordered everyone to return to the Marin Headlands and barricaded his people inside the base, ignoring the media's requests for a statement. 
That night, riots erupted all over San Francisco, fueled by both pro- and anti-mutant protestors. Cyclops and the X-Men tried to keep the peace, but they found themselves unable to contain it. As a result, Norman Osborn, his "dark" Avengers and HAMMER (formerly SHIELD) arrived in the city and put it under martial law in order to quell the rioting. Worse, at the end of the evening, Osborn called for Cyclops’ arrest—but Cyclops escaped, refusing to comply.
Immediately thereafter, it appeared that Emma defected to Norman's side, where she began leading her own team of HAMMER-sponsored X-Men—but this was all part of Scott's grand plan. 
During negotiations with Norman Osborn, Scott ordered him and his troops to leave the city, an order Osborn predictably refused. Cyclops told him he had his chance and departed. He then launched a multi-pronged plan to move the X-Men not just out of San Francisco, but out of the jurisdiction of the United States entirely. He formed one team of X-Men to free the mutants Osborn had taken prisoner, another team to neutralize Emma's team of "dark" X-Men, a third team hand-picked to take down Osborn's Avengers, and a final team to raise the sunken Asteroid M off the coast of California. When all of the pieces were in place, Emma betrayed Osborn and defected back to the X-Men with her mutant associate, Namor the Sub-Mariner, and several other Dark X-Men members.
Asteroid M, meanwhile, which had been submerged in the bay outside of San Francisco for several years, rose to the surface, just in time to be occupied by Cyclops, his X-Men, Emma's new recruits and all of the now-freed mutant prisoners, including the captured Professor Xavier. Declaring this floating rock their new home, Cyclops addressed the gathered media outlets and stated that since the U.S. clearly didn't want mutants within its borders, they were leaving. 
They now considered themselves a sovereign nation and said they didn’t want a fight and that no one had any reason to fear them. Obviously this wasn't good enough for Norman Osborn, who immediately launched an attack on the new island. Cyclops, however, had prepared for this and put his carefully laid plans in action, successfully neutralizing each member of Osborn's Avengers. With the battle clearly over, Osborn privately admitted defeat and departed, leaving Cyclops to declare to the cameras that all mutants would be free and safe on the island nation now known as "Utopia." [Utopia crossover]
Maintaining order and supporting life on Utopia proved to be a difficult task, as Cyclops not only had to worry about defending the island from outside attacks, but also about providing water, energy, and food to its inhabitants. A meeting with Mayor Sadie in which he demanded supplies and safe passage from the city quickly grew awkward. Even stranger was the unannounced arrival of Magneto on the island, who, surprisingly, came not to attack the X-Men, but to praise Scott for accomplishing what he never could: uniting the mutant race. Magneto kneeled before Scott and asked to join them on Utopia, a request Scott granted, despite the objections of Professor X. [Uncanny X-Men (1st series) #515-516]
Later, Cyclops tried to help Emma purge the malevolent entity called the Void from her body, where it had been ever since the climactic fight with Osborn's Avengers. However, he ended up absorbing the Void into himself. An "expert in repression," Scott managed to contain it within the black box in his mind, where he locked it away, hopefully forever. [Uncanny X-Men (1st series) #518]
Shortly thereafter, Beast confronted Cyclops and announced he was quitting the X-Men. He believed Cyclops had taken things too far and wasn't including anyone else's input in his decisions. Besides his professional concerns, Hank also felt personally betrayed by Scott during the rise of Utopia. Hank had been arrested early on in the Proposition X riots, and was held and tortured for days by Osborn and his people. Scott could have rescued Hank and the prisoners earlier, but chose to wait until the most "strategically beneficial" time to do so. Beast left Utopia and the X-Men, but Scott refused to let Hank's departure affect him. [Uncanny X-Men (1st series) #519, Uncanny X-Men: Heroic Age #1]
Scott's feeling that he was losing control of the situation only worsened when he learned that Magneto had singlehandedly solved a problem that had been plaguing Utopia since its onset. Angered, Cyclops reprimanded Magneto after their meeting and told him he would never trust him—a confrontation that prompted Magneto to nearly kill himself retrieving Kitty Pryde from deep space. [Uncanny X-Men (1st series) #521-522]
When Selene raised the dead mutants of the world and sent them to attack Utopia, Cyclops lost three of his people during the fighting. Thankfully, he was able to send X-Force to the source of the attack, where they destroyed Selene and neutralized the remaining undead mutants before any more of his soldiers fell. [Necrosha crossover]
Cyclops soon held a meeting with the X-Men where he revealed their time as a species was running out: the three mutant deaths during Selene's attack on Utopia meant there were now only 181 known mutants left on Earth, which was not enough to repopulate the species. Thankfully, Cable returned from the future at that point with Hope Summers, the mutant messiah, who was now a healthy young woman. Unfortunately, the X-Men were not the only ones who detected Cable's arrival in the present: Bastion and his armies of mutant-haters took note of his return as well. During the mission to get Hope safely back to Utopia, the truth about X-Force was revealed to the rest of the X-Men, and the X-Men’s teleporters specifically came under attack. Cyclops lost three of his best teleporters, including his old friend Nightcrawler, who died bringing Hope to safety. Kurt's last words to Scott were harsh ones, after he learned about the X-Force "kill squad," and his death weighed even more heavily on Scott because of this.
Although Cyclops was relieved to be reunited with Cable and excited to meet Hope in person, the X-Men's troubles were far from over. Donald Pierce, one of the X-Men's prisoners and Bastion’s inside-man, destroyed the X-Men's means of transportation, while the Purifiers eliminated the rest of their key teleporters. Cyclops executed Pierce without hesitation, but the damage was done: the X-Men were now trapped on Utopia, making them sitting ducks when Bastion activated a containment sphere that sealed them all within the vicinity of San Francisco. 
Bastion then unleashed wave after wave of Nimrod Sentinels into the containment sphere via a portal to a future timeline. Trapped and facing inevitable destruction, Cyclops concocted a plan to send Cable and X-Force into the future to eliminate the source of the endless waves of Nimrod Sentinels. Unfortunately, this was sure to be a one-way trip, forcing Scott to bid farewell to his son so soon after he returned. While X-Force was gone, the X-Men did their best to defend themselves against the Nimrod squadrons. Eventually X-Force completed their mission in the future and managed to return to the present through the portal the Nimrods had used, but one of their own—Cable—had to sacrifice his life in the process. Enraged at losing her father figure, Hope's mutant mimicry powers fully activated and she easily destroyed Bastion and his remaining minions, but she was not happy with Cyclops for sending his son (and her adopted father) to certain death.
In the aftermath of this saga, Cyclops disbanded X-Force and buried the remains of his son. Meanwhile, the fact that Hope, in whom he placed all of his faith in reviving the mutant race, 
was angry at him caused him further distress. However, Scott soon received a sign that his faith in Hope was not misplaced: she displayed something resembling a Phoenix Force energy signature, after which five new mutant signatures were detected on Cerebra. To Cyclops, this was proof that he had been right all along -- the mutant race would survive. [Second Coming crossover]