This issue is set before all of the current events happening in House Of X. This explains how Charles Xavier set up Krakoa. Xavier and Magneto have arrived at Bar Sinister. This is where Mr Sinister and his many clones base their genetic experiments. Xavier and Magneto come knocking to find one of his clones guarding the doorway.
Magneto quickly subdues him and they both walk inside. Sinister is sitting in his grand thrown room. Sinister's butler starts immediately commenting on Magneto's cape. This was a mistake as Mr Sinister is a huge fan of capes and orders the butler to be executed.
The proposal that Magneto and Xavier have brought is that Mr Sinister does some work for them. They want him to do extensive research into the mechanics of the mutant X gene. Sinister isn't really interested since he hasn't found any of the groundbreaking results he's famous for and this normally throws him off that specific field of research. Luckily, this isn't the real Mr Sinister.
Just for safety Charles erases the memory of the meeting they've just had but implanted the idea in Sinister's mind that he wants to do more extensive research into the mutant X gene.
We move a long a little bit to Charles Xavier introducing Cypher to Krakoa. Krakoa is a living island an Cypher is a mutant that can decipher any language. This includes the forgotten language that Krakoa speaks.
When Charles is showing Cypher the way though we notice that Cypher releases something when he's randomly touching plant life. The Legacy virus. The epidemic that caused mutants to lose control of their abilities.
Krakoa and Cypher come face to face. This is a big deal as we know that in the future that the X-men supposedly stopped, Cypher had merged with Krakoa after supposedly being injured in battle.
This is when Krakoa reveals its hidden history to Cypher. It didn't used to be called Krakoa. It was once a piece of land called Okara and it was attacked by creatures from the earth. They were wielding the Twilight sword that's featured in a lot of mystical based Marvel properties.
The attack tore Okara in two and they became two beings. One of which is Krakoa and the other is a being called Arakko. These monsters were formidable. But there was a "hero" at that time who saved Krakoa. He was and still is called Apocalypse.
Apocalypse made sure that his first iteration of the of the four horsemen of the apocalypse were there to guard the other side of the dimensional gateway. This did leave them stranded on the definition of a hellish landscape. Xavier leaves Cypher and Krakoa to become well acquainted.