With Teeth was always supposed to lead directly into the next record because of the unfinished "concept" slots from the Bleedthrough story, which TR didn't get around to actually writing enough songs to flesh out. Judging from what he said later, some kind of daydream he had on the tour bus that inspired Year Zero led to the Bleedthrough/With Teeth storyline-essay-thing about sobriety and political awareness being scrapped in its favour.
This is the only theory I've seen that explains why "The Warning" was one of the song titles on the With Teeth lyrics poster but has no visible lyrics under it: TR and Rob Sheridan got their thematic world-building ambitions for an apocalyptic time-traveling scenario from the Bleedthrough concept, which was a metaphor for "waking up" to a new feeling of presence after kicking booze.
Swap out the presence of sobriety with the Presence — and you have YZ.