BIOGRAPHY - Page 12
M-Day had yet another side effect beyond depowering mutants and inciting a virulent anti-mutant backlash: it triggered Cyclops’ forgotten brother, Vulcan, to awaken from his longstanding dormancy inside the orbiting island Krakoa. Gabriel returned to Earth, enraged at how much time had passed. Without knowing who he was, Cyclops and the X-Men tracked Vulcan down by following his powerful energy signature. 
From Vulcan, Scott learned about what had really happened on Krakoa: about meeting his brother Gabriel for the first time, about the second team of X-Men, about Xavier’s mind-wiping… everything. Later, Vulcan left the Earth and headed into space to get revenge on the Shi’ar Empire for what it had done to his parents. Scott, meanwhile, was understandably infuriated upon learning how deeply Xavier had betrayed, manipulated and misled him, further eroding his faith in his mentor and figurative father. He told Xavier he was no longer welcome at the school. [X-Men: Deadly Genesis #1-6]
Realizing that the X-Men had been too reactive lately, Cyclops decided to give Rogue full control over her own strike force of X-Men to deal with threats in the field before they found their way to the school. Rogue's handpicked team of X-Men included not only reliable X-Men like Iceman and Cannonball (and Cyclops's son, Cable), but also her treacherous mother, Mystique—whom Cyclops had reluctantly granted a second chance and was now staying at the X-Mansion—along with a few other wild-cards. Cyclops didn't understand her reasoning but ultimately decided to trust her judgment. He even defended her when Professor X, who continued to linger around the school, suggested she be reprimanded for her reckless behavior. [X-Men (2nd series) #188-193]
When Mystique inevitably betrayed the X-Men, she and her cohorts, the Marauders, took down not only Rogue's entire team, but Cyclops's team as well. Only Iceman and Cannonball managed to escape the ambush, at which point they learned that the Marauders, acting on orders from Mr. Sinister, were eliminating anyone and anything that had direct knowledge of the near future. Also on their list was Cable, who seemingly died when the Marauders blew up Providence, his headquarters. [X-Men (2nd series) #200-203]
While grieving about his son's apparent death, Cyclops struggled to figure out what upcoming event Mr. Sinister was trying to prevent them from perceiving in advance. He realized he needed all X-Men on deck since something big was obviously about to happen. But what this incident also made him realize was that he had erred in giving Mystique a second chance, and that the X-Men needed to be more ruthless in the future if they intended to survive. [X-Men (2nd series) #204]
On top of dealing with losing Cable, Cyclops also learned from Havok that their father, Corsair, had died in space during the fight against their other brother, Vulcan. Scott had already felt like he had lost one father figure due to the recent revelations about Xavier, and losing his actual father on top of it was almost too much for him to deal with. Struggling to cope, he found comfort in some words from a surprising source—Logan—and contacted Alex to talk about their father together. [Marvel Comics Presents (2nd series) #8]
With everything that was going on with the X-Men and mutants as a whole, Cyclops also didn't feel like he could fully count on Emma, whom he still resented for abandoning the team during their confrontation with Danger. Emma confronted him one evening in their room about his distrust and began mentally deconstructing him. 
She called out his lingering feelings for Jean and tore into his insecurities about Logan being more popular than he was, about his feelings of mediocrity within the X-Men, about Xavier pitying him for being so unremarkable and, finally, about his lack of control over his optic blasts. Emma confronted him about a memory he had long repressed: as a child, he had decided to let his optic blasts rage out of control in order to give himself something to worry about controlling, all so he could take his mind off of how powerless he felt about the direction of his life. Scott could not deny it when faced with this memory. As a result, his mind broke. While his optic blasts no longer fired when he opened his eyes without his ruby quartz visor, Scott had no mind left with which to control them or his body. Emma had reduced him to a vegetable. [Astonishing X-Men (3rd series) #13-14]
Although he appeared to be in a catatonic state, however, Cyclops was able to observe what was happening around him, even if he couldn't respond. Scott idly watched as Emma told the rest of the X-Men that something was wrong with him, before luring them all into psychic traps against different manifestations of her fractured personality. Somehow, Cyclops managed to regain control of himself and confronted Emma right after she had taken out the rest of the team and accomplished her goal. 
Realizing that the people the rest of the team were seeing were Emma's psychic illusions, Scott, still unable to access his optic blasts, began shooting them with a gun until only the true Emma remained. After his teammates were free from Emma's control, he explained what was going on: Emma, wracked with survivor's guilt because she had lived through the mutant genocide on Genosha, had been manipulated by the captive Cassandra Nova into letting her out of her inescapable prison. Now that Emma had manipulated Kitty into freeing Ms. Nova, Cassandra began transferring her consciousness into a new host. While Cyclops confronted Emma about this and explained it to the team, however, they were all ambushed by Ord and Danger, who had teamed up to eliminate the X-Men. Luckily, the X-Men were rescued when they were all transported by SWORD to one of its space crafts. [Astonishing X-Men (3rd series) #15-18]
Once aboard the ship, Agent Brand contained Ord and Danger and informed the X-Men they were running out of time to save the Earth from the Breakworld, who believed Colossus was the specific mutant destined to destroy their planet. While en route to the hostile alien world, Brand enacted a plan she hoped would divert the Breakworld warships that were already on their way to Earth. 
Her plan worked too well, however, and their ship came under attack, forcing Brand and the X-Men to escape to the Breakworld on lifeboats. Once separated from the rest of the team, Cyclops and Emma had to spend some time alone together. Scott revealed that, despite what had just happened with Cassandra Nova, the psychic therapy they endured made him love her more than ever. [Astonishing X-Men (3rd series) #19-21]
When the X-Men learned that the Breakworld’s backup plan to eliminate Earth was to fire a giant bullet at it from across the universe, they took action to dismantle the weapon. Cyclops concocted a daring scheme in which he infiltrated Ord's forces from within by allowing himself to die in the vacuum of space, full well knowing—and hoping—
that Ord would use the advanced technology of the Breakworld to resurrect him so he could torture him for information. Sure enough, he did, and Scott was brought back to life as Ord's prisoner. Once everything was in place, Cyclops revealed to Ord that he not only tricked him, but also that he actually did have access to his mutant power—which he demonstrated by unleashing a massive optic blast at his captors. Successfully catching the forces of the Breakworld off-guard, Cyclops ordered the X-Men to execute their final attack on the alien army. Unfortunately, the squad in charge of dismantling the weapon pointed at Earth failed in its task before the Breakworld fired the bullet, with Kitty Pryde still inside of it. [Astonishing X-Men (3rd series) #22-24]
Neither Cyclops's team of X-Men nor the heroes of Earth were able to stop the bullet as it approached its target. Although Cyclops and Emma were not able to get Kitty out of the bullet before it reached the Earth, the complication provided an opportunity when Kitty used her power to phase the gargantuan bullet through the planet. Unfortunately, in the process, Kitty became permanently bonded with the projectile as it continued on its way through the vacuum of space. 
Cyclops's team saved the day, but they lost one of their dearest teammates in the process. As the team slowly recovered from this trauma, Cyclops found that he was slowly losing control over his optic blasts again and accepted back the burden of his ruby quartz visor—and all that it entailed. [Giant-Sized Astonishing X-Men #1]