Part of this show just don't make sense!
He Who Remains founded the Time Variance Authority to protect the Sacred Timeline and prevent the formation of a new Multiverse. He created the Temporal Loom as a failsafe to maintain the Sacred Timeline. The Temporal Loom would delete the branched timelines and destroy the TVA. The Kang variants would find each other, and another Multiversal War would occur.
At some point, He Who Remains allowed 63 new timelines to branch out. It would have made sense if Marvel Studio did this to show there have been multiple incarnations of the multiverse, and the TVA keeps getting formed time and time again because the Multiversal War keeps repeating. Each time, a different version of Kang creates the Sacred Timeline.
Except that's not what they did, and I can't understand why. He Who Remain had to have the TVA prune these timelines before the Temporal Loom had to reset everything. So why did they show the 63 timelines branching off or the TVA pre-Time Keepers? It serves no other value than to establish Loki's time slipping, which could have been done in an arguably much less confusing way.
And that's just the tip of the iceberg! In season one, the TVA was incredibly worried about timelines "red-lining," as that was the point at which a timeline could no longer be pruned. The Bombing of the Sacred Timeline was thought to be very serious because it threatened another Multiversal War. Yet Gernal dox was able to (relatively easily) prune dozens of timelines that had red-lined.
Furthermore, it was established that only one variant of Kang existed on the Sacred Timeline, a man named Victor Timely. Being born in the mid-1850s, Timely lacked many resources that would be necessary for him to discover the Multiverse. Thus, a Multiversal War could never happen. But when Loki and He Who Remains discuss the Temporal Loom, he explains the Temporal Look would delete all the timeline, and countless of his variants were already "out there" (on the Sacred Timeline). One of them would recreate the TVA (again, I don't understand why they didn't use Loki's time slipping to show this has happened countless times.) But perhaps only the benevolent variants of Kang were allowed on the Sacred Timeline.
Why was the Temporal Loom even created? I understand it powered the TVA, but He Who Remains said it was designed as a failsafe. If the multiverse began again, it would delete all the branched timelines AND destroy the TVA. Without the TVA, new timelines would imminently be created. All the Temporal Loom does is kill innocent people for no reason at all. Marvel Studios could have used this to show how evil He Who Remains was, but they didn't, and I can't figure out why! The Temporal Loom was the most confusing part of season two and didn't even serve a purpose.
Why did Loki have to keep the timelines alive? In destroying the Temporal Loom, he killed all the timelines. But why? If he had let the Temporal Loom do its job, the Sacred Timeline would have been intact, and the Temporal Loom would have been destroyed either way.
He Who Remains' replacement plan doesn't make sense either. He asked Miss Minutes to make Victor Timely his replacement should he die. Why, then, did he try so hard to recruit Loki and Sylvie? Apparently, he had many variants of himself he could have chosen from.
Anyways, these are just some of the things I find don't make sense about this show. I really loved the first season, but this season just didn't make much sense.