The full story
Loki comes back from the end of time with a problem: he's time slipping, jerking between past, present and future with no control over it. The TVA is in chaos. With He Who Remains dead, the timeline is branching faster than anyone can prune it, General Dox wants the new branches destroyed, and Ravonna Renslayer has vanished along with Miss Minutes, the TVA's animated mascot.
Loki and Mobius take the slipping to Ouroboros, "O.B.," the TVA's repair technician and the author of its handbook. With his help, Mobius pulls Loki out of the time stream and steadies him. They track down Hunter X-5, who has deserted and is living as a film star called Brad Wolfe in 1977 London, and he leads them to Sylvie, working at a McDonald's in 1982 Oklahoma. Dox goes ahead anyway and destroys most of the branched timelines with reset charges.
The Temporal Loom, the machine at the heart of the TVA that weaves time into the Sacred Timeline, is overloading under all the new branches, and only He Who Remains could fix it. The next best thing is Victor Timely, a variant of his: a nineteenth-century inventor in Chicago, whom Renslayer and Miss Minutes reached first, slipping him the TVA handbook as a boy. Miss Minutes reveals what she's been hiding. Renslayer was He Who Remains' general, and meant to be his partner, before he wiped her memory. Renslayer and Miss Minutes try to take over the TVA. Dox and her loyalists refuse to join them and are killed, and Sylvie has an enchanted Brad prune Renslayer.
Timely is brought to the Loom with O.B.'s Throughput Multiplier, but the Loom's radiation tears him apart, and the Loom explodes. Loki is left alone. The TVA is gone, and his friends are back in the lives they had before it took them: Mobius selling jet skis as Don, B-15 a doctor named Verity Willis, Casey the convict Frank Morris breaking out of Alcatraz, O.B. a science-fiction writer called A.D. Doug. Loki learns to control his slipping and goes back, again and again, to save the Loom, until He Who Remains tells him it was never meant to hold. It's a failsafe, built to burn away every branch and leave only the Sacred Timeline.
Loki chooses another way. He walks out to the Loom, destroys it, and holds the dying timelines together himself, gathering them into the shape of a tree, with himself at the end of time keeping it alive. The TVA rebuilds to protect the branches instead of pruning them, with B-15 among its leaders, and watches for He Who Remains' variants. Renslayer wakes in the Void, facing Alioth. Mobius leaves the TVA, and he and Sylvie watch Don's children from a distance.