Krakoa is believed to have been a very small island in the Pacific Ocean that was located close to where some nuclear bombing tests were done. It was thought that the radiation somehow turned the island's ecosystem into a single hive-mind entity. Today, it is the living nation-state where all persons with the mutant gene are invited to live on.
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History
Krakoa was once part of a greater land called Okkara, but it was attacked by an enemy wielding a twilight sword. Okkara was split into two creatures, Krakoa and Arakko. Apocalypse arrived with his First Horsemen and sealed away the enemy. However, both Arakko and the Horsemen had to be sealed away with them, leaving Krakoa feeling mournful and lonely.
Nick Fury along with his team accidentally witnessed the explosion on Krakoa in 1945. Soon after that they crashed on the island where they came across the island's collective intelligence. In order to leave the place Fury managed to arranged a peaceful parting in exchange for keeping its existence a secret.
The X-Men (then consisting of Cyclops, Angel, Havok, Iceman, Marvel Girl (Jean Grey), and Polaris) came to the island after Cerebro detected an unknown mutant there, and were captured by Krakoa, who used them as food sources.
Another team of young mutants, composed of Petra, Darwin, Sway and the third Summers brother Kid Vulcan, from a parallel X-Mansion led by Moira McTaggart, were sent to help the original X-Men. They managed to save Cyclops and returned him to Professor X. However, Krakoa killed Petra and Sway and left Darwin and Kid Vulcan almost dead. Xavier erased all records of the real events and his brother from Cyclops' mind, and altered the other mutants' minds to cast the illusion of a speaking, sentient Krakoa.
With the failure of the first team Professor X then decided to recruit international mutants to save his X-Men, namely Colossus, Nightcrawler, Storm, Sunfire, Thunderbird, Banshee, and Wolverine, and sent them to Krakoa. Cyclops' group of mutants paired off and after each pair encounter and defeated various aspects of the island, the new X-Men team found the original X-Men, who were weakened from being fed upon by Krakoa for so long. At this point, it was revealed that the island was itself the mutant they had originally detected and Krakoa battled the new and old X-Men by forming a giant humanoid body out of its terrain. With a combination of psi interference by Professor X and energy blasts from Cyclops and Havok, Storm was able to supercharge Polaris' magnetic powers with bolts of lightning. Polaris interacted with the Earth's core and created a magnetic pulse so strong that she was able to launch Krakoa into outer space. The X-Men—then counting thirteen members—were saved. He was captured by the enigmatic alien, the Stranger, and were imprisoned in the Stranger's Labworld for the alien to study him. He remained their until freed by Overmind.
A portion of Krakoa's biomass was used for construction of the biosphere at the Massachusetts Academy, nicknamed the "Danger Grotto" by Generation X. A "son of Krakoa", the result of a spore that was released from Krakoa as it was shot into space, later appeared. Nightcrawler eventually defeated this "Vega-Superior" by tricking him into drowning himself. The Young X-Men encountered another "Krakoa" when 56 construction workers disappeared from a construction site on a tropical island. It is unclear what the relation between this Krakoa and the original is, if any.
After apparently abandoning his dream for peaceful coexistence, Professor X ultimately repurposed Krakoa into a sovereign nation state for mutants. Now donning a portable Cerebro, Xavier seemingly recruited and experimented on Krakoa with the help of Cypher. Both expanding Krakoa's consciousness and cultivating its biome to include exotic flowers that can be used for various purposes, as such becoming the primary economic resource. These Flowers of Krakoa could grow Habitat, self-sufficient offshoots of Krakoa that served as embassies around the solar system, while remaining connected to its hive mind via Gateways, which provided ways to instantly travel from one part of Krakoa to another. Additionally, Xavier bought world leading pharmaceutical companies with his vast wealth to produce three new super drugs from Krakoan flowers, offering them to every country that formally recognized Krakoa as a nation. These drugs—dubbed I, L, and M—operate as a adaptive antibiotic, extend the human lifespan by five years, and prevent human "diseases of the mind" respectively, allegedly hereby solving the devastating health problems in humans. Professor X, Magneto, Moira MacTaggert, and a large number of former X-Men allies and enemies then joined the sentient island to form a mutant nation.
An island known as Arakko later appeared off the southern coast of Krakoa. With Cypher offworld, Cable and Prestige accompanied their father in exploring the new landmass and learned about it from the High Summoner of Arakko before the two islands merged into one.
