Both Genesis and Angel's stories come out of the (incredible) Uncanny X-Force title. (Sub-par? Apocalypse? X-Factor? Are we reading the same book?) A little rundown: Wolverine and crew discover Apocalypse's cult are training his new incarnation. They discover it's a 9 year-old boy. They dissemble on what to do about him til Fantomex shoots him in the head. The team continues to be conflicted about this turn of events until much later (15 or so issues) when Apocalyplse begins manifensting himself inside Archangel. The team tries to gather Celestial Life and Death seeds (involving a jaunt to the AoA universe to grab one where they discover that universe's Logan ended up becoming Apocalypse). Warren's goal is to get the seeds and combine them with The World to create a fast-breeding test-bed for evolution, and basically run the world through rapid iterations of it doing what Apocalypse does. During this, Fantomex reveals that even Kid Apocalypses don't die easy from headshots, and Fantomex had him raised in secret (maybe in The World, don't recall) by a nice midwestern couple to be a regular kid.

edit: why did I keep spelling Fantomex like that?