BIOGRAPHY - Page 19
Eight months passed. During that interim, Cyclops established what he deemed the X-Nation at the Weapon X facility. He reprogrammed Sentinels and had them stand guard over his base, and opened it up as a sanctuary for mutants all over the world. Mutants under the protection of X-Nation were considered untouchable by SHIELD officials. [Avengers (5th series) #37]
During this eight-month period, it was also revealed to the people of the world that the multiverse was dying. Earths from alternate universes were colliding with each other during events called "Incursions." At the end of an Incursion, two parallel Earths would occupy the same space and, as a result, both of their respective universes would instantly be destroyed—completely vanishing from existence. However, destroying one of the colliding Earths would spare both universes, at least until the next Incursion arrived. Scott's former colleague Namor had created a team of amoral warriors who were more than willing to destroy the incurring Earths in order to save their universe. Terrax the Truly Enlightened, a member of Namor's Cabal, had broken the news of the multiversal collapse to the United Nations, but assured them and the people of the world that the Cabal was taking care of the hard part, allowing everyone else to continue living their lives with clean consciences. [Avengers (5th series) #35, New Avengers (3rd series) #24, Avengers (5th series) #37]
As the multiversal collapse continued, Cyclops reached some sort of truce with Beast and allowed him to use his Weapon X facility for his research. Because the survival of his native reality was by no means assured, Scott began preparing a backup plan he hoped would allow mutants to emerge intact. Somehow, Cyclops acquired a Phoenix Egg, which he intended to use save mutantkind. 
When Sunspot and Cannonball—once New Mutants, now Avengers—asked what he had planned, he cryptically said it was long past time he got in the game. Later, as the final Incursion neared, Sunspot and Cannonball grew desperate for Scott's help, reminding him he was a hero who had always devoted himself to saving mankind. At that point, however, Cyclops corrected them. He stated that when he had said it was time to "get in the game," they misunderstood what he meant. He was finished making sacrifices trying to save an ungrateful humanity. Now, he had other plans, and those plans weren't to save the world; the name of the game this time, he said, was resurrection. [Avengers (5th series) #38, 42]
Eventually, the Incursion saga reached its inevitable end as the last two remaining Earths prepared to collide with each other. One was Earth-616, while the other was Earth-1610—the Earth of the Ultimate Universe. Neither of the two Earths were willing to go down without a fight. As the ruthless forces of Earth-1610 invaded Earth-616 through the Incursion site in New York City, Cyclops arrived at the battlefield with his army of reprogrammed Sentinels and his Phoenix Egg, 
which he housed in a containment unit. What he had planned remained unclear, however, as time truly ran out before he could put his plan into motion. A desperate team of superhero scientists executed a last-ditch effort to salvage a portion of mankind that could hopefully survive the Incursion. As part of their plan, the mutant known as Manifold used his teleportation powers to pull in a selection of humans and mutants that would restart the human race—and Cyclops was among the select few chosen. As his body was pulled into a life raft specifically designed to withstand the final Incursion, Cyclops merged with the Phoenix Egg and once again became the Phoenix. [Secret Wars #1]
Miraculously, the life raft passed through the final Incursion largely intact. The raft and its survivors emerged on Battleworld, the patchwork planet that a cosmically empowered Doctor Doom had compiled using remnants of dying worlds he had salvaged. Doom's servant, Doctor Strange, 
found the life raft five years after the formation of Battleworld and kept it hidden in his sanctum sanctorum. Three years later, after an identical life raft housing Namor's Cabal was unearthed on Battleworld, Doctor Strange finally decided to pull the one he found out of stasis. Cyclops, now merged with the Phoenix, was among the few heroes who emerged from this life raft, along with Mister Fantastic, Black Panther, Star-Lord, Spider-Man, Captain Marvel and Thor.
After explaining where they were and what had happened, Strange brought this collection of heroes to help assist an army of Thors against Namor's Cabal. Soon, God-Doom himself arrived at this battlefield and explained to the assembly of heroes and villains that it was he who had saved everything and he who was now God. Cyclops, empowered by both the Phoenix and his own pro-mutant ideology, refused to kneel down to God-Doom. Believing himself to be Doom's equal in power, he attacked God-Doom with the full power of the Phoenix Force. Scott appeared to have the advantage, initially—until Doom reached out, grabbed Cyclops by the throat and snapped his neck. Cyclops's lifeless body slumped to the floor, putting an end both to the life of Scott Summers and to the Phoenix Force. [Secret Wars #3-4] As with many deaths caused during this period, however, Cyclops was restored to life when God-Doom fell and Reed Richards assumed the power to restore the multiverse. [Secret Wars #9]
Life with the X-Men continued until Cyclops' team received an emergency broadcast from Jamie Madrox on Muir Island. On the island, they found it covered with Terrigen Mist, one of two clouds released into Earth's atmosphere by Black Bolt of the Inhumans some months earlier. Jamie, and all the mutants on the island, were dead. The mists had mutated in the atmosphere, becoming a substance that was still transformative to Inhumans and benign to humans, but was now hazardous to mutants. Dubbed "M-Pox," exposure to the mists could do nothing at all to mutants, make them sick, or kill within minutes. Cyclops experienced this final fact first hand. Minutes after entering Muir Island, Scott collapsed and died alone in Emma's arms. [Death of X #1]
In a state of shock and rage, Emma enacted a desperate plan to save the mutant race and preserve Scott's legacy. She used telepathic illusions to convince everyone Cyclops was still alive and used Scott's image to publicly attack the Inhumans for their "death clouds" and rally mutant support around "him." Emma and "Scott" successfully destroyed one of the Terrigen clouds, but drew the ire of the Inhuman Royal Family. Emma had "Scott" commit suicide by challenging Black Bolt directly, having the leader of the Inhumans kill the leader of the mutants for all the world to see. [Death of X #2-4]
[Note: It must be said that Marvel clearly had no idea "What Cyclops did" when they first relaunched after Secret Wars. Cyclops' apparent actions in Death of X amounted to alerting the public about M-Pox, destroying a cloud and getting himself killed. There was ultimately never a clear explanation about how this led to him being declared a universally reviled terrorist figure in the public eye.]
The original five X-Men would ultimately overstay their welcome in the present, risking all of space-time by not returning to the past. This led a teenaged version of Nathan Summers to intervene for them, pushing the group to return to the past. At the same time, however, "Kid Cable" had his own wrong to right, and put into motion events to bring Cyclops back to life. He found an engineer named Paul Douek, whose life Cyclops had saved years ago. At Cable's direction, Paul was able to reverse-engineer and miniaturize the Phoenix Cage technology Tony Stark built during the Phoenix Five affair. After Cyclops died on Muir Island, Kid Cable surgically inserted the Cage-tech implant in Scott's corpse. When the Phoenix Force temporarily restored Cyclops to life during its resurrection of Jean Grey, the Phoenix Cage captured a portion of the Phoenix energy, allowing Kid Cable to trigger it and bring Cyclops back to life permanently.
Kid Cable kept Cyclops isolated until he could complete his work sending the original five home. Cyclops was deeply conflicted about Kid Cable killing the older version of Cable during his mission, as well as the rush of “new” memories he received when the time loop ended and young Cyclops's experiences came back to him. In hindsight, Scott came to believe that his mutant revolution and militant protection of mutantkind was a reaction to the Decimation, but ultimately wrong. He resolved to do things differently this time around.
Kid Cable agreed, but also needed to verify Cyclops's change of heart. The X-Men were facing their final battle with the Omega-class power of X-Man and Legion, a battle that would lead to the end of the X-Men. However, Kid Cable had also arranged for Tavin Tierney (the mad scientist Cyclops once saved Paul Douek from) to find Douek and attack his family at the same time. The future of mutantkind, or the life of one man with his wife and son. Which would Cyclops choose? Scott no longer saw human life in terms of “acceptable losses” and saved Paul's family from Tierney's robot hordes. [Extermination #5, Phoenix Resurrection: The Return of Jean Grey #5, Uncanny X-Men (5th series) Annual #1]