Fey and Izzy return the Doctor to Gallifrey, where he enters the Matrix to save himself. When an Academy dropout takes an unhealthy interest in him, the Doctor and his companions are lured into a society that threatens the existence of Gallifrey... and Rassilon himself.
In the Endgame trade paperback, Alan Barnes stated this was both meant to be a return to the strip's version of Gallifrey - "'our' Gallifrey, as opposed to the arcane Looms and Houses of the New Adventures" - and a large "US comics-style Event" to prelude the Doctor's fake regeneration.
Part of the plot, including an entire chapter, were cut from the story. Barnes would go on to turn the visuals and ideas from that chapter into his audio drama Neverland.