The complete truth about Krakoa's origin is unknown, however it is believed that Krakoa came to be as a result of nuclear experiments in the Pacific Ocean. When Professor X detected a powerful mutant signal on a remote island in the middle of the pacific using Cerebro, he dispatched the original team of X-Men to investigate. It would turn out that the island Krakoa was the mutant that Xavier detected. Krakoa would capture the X-Men in order to feed off of their strong mutant energies. Xavier would send two other rescue teams to bring back the X-Men. The first consisted of young and inexperienced mutants that Krakoa was able to defeat quickly. The second rescue team consisted of older mutants from around the globe. The second team would defeat Krakoa and rescue the team. Krakoa was lifted into the orbit by Polaris. Krakoa was last seen as part of the Stranger's cosmic collection.
Spores from the launched Krakoa made their way back to earth in the original Excalibur series. They collected to form a minor consciousness that fought against a solo Nightcrawler.
Krakoa is the combined form of all animal and vegetable life as well as the mineral/soil of the island itself. It was originally believed that Krakoa possessed sentience, however belief was created by Professor Xavier when he wiped the minds of his X-Men involved in the Krakoa incident and replaced all of their memories of the occurrence with new ones. Krakoa cannot actually speak or understand language and does not seem to actually act out of conscious thought. Instead Krakoa simply wails and groans and acts primarily out of instinct to what occurs around it. For instance, capturing the X-Men was not a conscious decision to drain their power, but instead was a low level reaction based on the power the X-Men possessed. Krakoa possessed the natural instinct to feed and when presented with the opportunity reacted instinctively upon it.
Krakoa controls all of the very environment of the island mass, using plants and animals alike as an extension of itself. It can also re-arrange the land mass of the island in in almost any way including constructing a crude, bipedal humanoid form with which it used to attack the X-Men. Despite its lack of intelligence, Krakoa is a powerful creature. Originally, Krakoa was also depicted as possessing massive psionic power (enough to rival that of Xavier himself), although this may have only been part of the memory that Xavier created in the X-Men and not founded in reality.
The Big Ret-Con - Deadly Genesis
One of the biggest ret-cons in the history of Marvel comics (probably second to Jean Grey's NOT being Dark Phoenix) was when Marvel decided that the events of Giant-size X-men #1 didn't happen the way we think. There were lots of effects that came out of this massive alteration of history.
- We finally learned of the 3rd Summers brother (Vulcan) which was hinted as far back as X-men Vol. 2
- Krakoa was not a sentient lifeform but just a collection of impulses and urges stemming from radiation (although the son of Krakoa in Excalibur was shown to be intelligent.
- We find out that Storm's team was not the second group of X-men, but the 3rd after Vulcan, Petra, Sway and Darwin.
- Cyclops wasnt freed by Krakoa, he was freed by the second group of X-men before they were defeated.
- This is the beginning of the dissolution of the relationship between Scott and Charles.
Dawn of X
After revelations shared by Moira MacTaggert, Pr. X and Magneto tamed this one time enemy of the X-Men into an island nation for all mutants. Using Krakoa's many natural resources they were able to create teleportation gates around the world to connect them to the global mutant population and universal cures to placate other nations into recognizing their autonomy.