The issue serves as a link between the original X-Men and a new team of X-Men.
Chapter One: Second Genesis - It's the introduction of new X-Men, called by Xavier one by one: Nightcrawler (he escaped from an angry mob from a small village in Germany with help of Prof. Xavier), Wolverine (from governmental facilities in Canada), Storm (who believed she was a Goddess in Kenya and helped locals with rain), Colossus (from a crop field in Siberia, where he had just saved his young sister Illyana from a runaway tractor) and Thunderbird (from a reservation on Arizona) and the already known Banshee and Sunfire.
Chapter Two: ...And Then There Was One - Cyclops tells the new X-Men about what happened to the old team. Cyclops, Angel, Iceman, Marvel Girl, Lorna Dane and Havok ( Beast had left X-Men before the mission) had discovered a new mutant menace in an island in the South Pacific - Krakoa. When they arrived, something strange happened and the only thing Cyclops remembered is that he awakes without his powers inside the X-Jet, going back on auto-pilot to the mansion. That's why Professor Xavier called all these new mutants, to help the X-Men.
Chapter Three: Assault Force - The new X-Men team are heading to Krakoa, with Cyclops as their leader. He divides the group into four pairs, and they all face different problems after landing: Cyclops and Thunderbird have to defeat a living tree, Storm and Colossus have to destroy a living avalanche of rocks, Banshee and Wolverine battle against two giant lobsters and Nightcrawler and Sunfire were attacked by giant birds. They all succeed on their battles and go to an old temple in the middle of the island. There they break a big wall and enter the temple, where they find the rest of the X-Men - Iceman, Marvel Girl, Angel, Lorna Dane and Havok - trapped on strange roots. After they release them, Havok tells Cyclops that the island of Krakoa is alive, and that it wants to capture them all.
Chapter Four: Karakoa...The Island That Walks Like A Man - The island Krakoa is alive and wants the X-Men to drain their energy and feed itself. That's why Krakoa had released Cyclops, to go get more mutants to the Island. The X-Men start to use all their powers on the Island, but no one is able to battle it. Then, Professor Xavier mentally appears, and uses his mental powers on Krakoa, while he tells Cyclops his plan. Storm starts to use all her powers to drain the energy of lightening on Lorna Dane, who starts to accumulate the magnetic power. The rain let the Island grow bigger and send Xavier astral form back to the mansion. Then, Cyclops and Havok use their powers on Lorna and the magnetic waves reach Earth's interior, causing the island of Krakoa to erupt to space. In the local where Krakoa used to be, a giant whirlpool appears, jeopardizing the X-Men. Iceman creates an ice globe surrounding them and they manage to escape safely.
At the end, Angel says to everyone: "What are we going to do with 13 X-Men?"
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.