I don't know how some of y'all are still confused about the timelines (outside of the after-credit scene).
Arnold creates Dolores, suicides by host.
Dolores and Ford create Bernard in the Cradle.
In Bernard's years he visits the Forge many times to create Eden.
S1 happens.
Dolores goes on a rampage, wiping out the Cradle.
Everyone heads to the Forge.
Dolores deletes most (not all) of the guest data in The Forge.
Hosts begin uploading to Eden.
Dolores is shot/keystone is hidden in her.
Valley floods.
Charlotte shoots Elsie (worst part of the entire series), Bernard replaces her with Delores-in-Hale.
Bernard scrambles his memory.
Data extraction team arrives, find all host bodies in flooded Valley brainless.
Discover Bernard is a host.
Human team arrives at Valley, Dolores-in-Hale is revealed.
All of the Host data is beamed away.
Dolores-in-Hale shoots Bernard to pluck out his brain, smuggles him and others to the real world.
Ford set up Arnold's house as a base for the hosts, Dolores uses it to recreate bodies for herself, Bernard, and whomever is in Hale now (maybe Teddy?)
As for William, I think he went down to the Forge and Downloaded his and his daughter's data. He recreates her, and she later in the future recreates him. (after-credits)