As explained in this answer, the TVA (Time Variance Authority) exists in a "Supreme Timeline" which is "above" the timelines which they overrule. They are "outside of time", in the sense that they live in a time of their own, and can look at the timeline(s) of the regular world.
But if this is the case, then why was it changed by the end of episode 6 of Loki?
I realize that this might be explained in season 2, but I have a feeling I just missed something.
I believe you're going to have to wait until something else in Phase 4 or season 2 of Loki itself for a definitive answer. At the moment though we have two conflicting pieces of information from Marvel themselves so it seems it isn't finalised yet.
Farahani, the production designer, has stated that Loki was actually sent to a different timeline. This would mean then that the TVA exists in a higher level outside of time but only outside of time to their own timeline, sort of like Sakaar or the quantum realm. In this case it isn't that the TVA is affected, it's that we're actually in a different TVA.
Farahani reveals that the look and design of the Kang statue was a game day decision designed by the in-house VisDev team. He assures Marvel.com that the entire set dressing of the TVA architecture was identical to the TVA we started the series with, in order “to delay the audience and Loki’s understanding that they were in a different place, that they were in a different timeline.”
Marvel, Loki: Deconstructing He Who Remains’ Life’s Work at the Citadel at the End of Time
Hiddleston gives a slightly different explanation in that the TVA we're in is the same as we've seen previously but it has been changed. He doesn't explain how this happens though. I will note though that outside of time doesn't mean it can't change at all. Kang, or another He Who Remains variant, could have changed things at the TVA without re-writing it all. Note that they have all the technology to do this including TemPads, Reset Charges, variants etc. We also don't really know how long Loki was sat down in the Time Theatre.
It’s a good plan that quickly goes sideways. No sooner does he reach Mobius and Hunter B-15, “He realizes that in the time he's been sitting on that step, something has changed.”
“Something has changed reality, including the reality of the TVA,” Hiddleston says. “The three statues of the Time Keepers are no more. In their place is a statue of Kang. And that his friend Mobius doesn't recognize him and doesn't know who he is. His destabilization in that moment is profound.”
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Kate Herron has since gone on record to say something similar to both Farahani and Hiddleston in that it's a different TVA but the same. The reality of it has changed because of what has happened.
Since the TVA resides outside of time, what can you say about the mechanics of the final scene?
So the way I see it in my head is that the TVA exists outside of space and time, but reality and everything as we understood it has completely changed in the last few minutes. With the multiverse branching, how do we know the TVA still exists in that way? We don’t know, and I suppose that’s a big question that will be answered as the show goes on. But in my head, the intention is that Sylvie thinks she’s sending him back to the TVA, but because of the way time and branches are crossing each other outside the window, Loki has unfortunately been sent back somewhere very different. So reality has shifted just by the nature of what He Who Remains said, and the idea is that he’s in this alternate TVA now.
As shown in the first episode of Loki season 2, “Ouroboros”, when Sylvie kicked Loki into a time door, he was sent into the past TVA. From there, Loki “time slips” back and forth between the past and present TVA. Loki theorizes that this happened because Sylvie used the TemPad of He Who Remains, the creator of the TVA.
Loki eventually learns how to control his time slips, and spends centuries time slipping in the TVA, a la Groundhog Day. In the season 2 finale, we discover that Loki’s time slips were actually part of He Who Remains’ plan, in order to manipulate ("pave the road" for) Loki to "make the hard choice" regarding the multiverse and the Sacred Timeline.
So, the TVA does exist outside of time for most beings, but He Who Remains has the power or technology to enable people to travel through time within the TVA, which contradicts the time travel rule in Avengers: Endgame. As Bruce Banner said in Endgame, “If you travel to the past, that past becomes your future, and your former present becomes the past, which can’t now be changed by your new future.” This rule doesn’t apply to time slipping within the TVA.
Relevant dialogue:
Mobius: Okay, and Sylvie kicking you through the Time Door into the past, that somehow started all this?
Loki: All I know is I was in the past. It was He Who Remains' TemPad, so maybe that's how it was possible.
While the TVA exists in a region separate from the Sacred Timeline, that region itself came into existence as a result of the actions of He Who Remains, within the timeline-bound multiverse. After Sylvie kills Nathaniel Richards (He Who Remains) the entire timeline is freed from stabilizing control and history returns to its previously chaotic form, reinstantiating the entire multiverse including the multiverse war, allowing an entirely different variant of Nathaniel Richards (possibly Kang the Conqueror) to emerge as the winner. Whichever variant wins will go on to create the TVA... which will then be separate from the new Sacred Timeline enforced by the new boss.
As is often the case when messing with time, this makes little sense to time-bound minds like ours. If it made any kind of sense at all then I'd be asking why Loki manages to remember things as they were instead of retaining his memory of the TVA as it was before the new instance. I guess we can hand-wave it away as an effect of having been in the Citadel at the End of Time at a critical moment.
Presumably at some point Kang will reach the same point as He Who Remains and set up the conditions for a Loki variant - or some other Hero - to come and finish him off, letting the entire cycle start over... until we eventually end up with a Nathaniel Richards variant who either abdicates to a machine or feeds the entire timeline to Alioth. It'll probably be replaced with something even more incomprehensible.
One thing of note to consider with regards to the "time of their own" - as I understand, we never see it being represented in the timeline viewer showing the TVA itself get close to Red Lining, like how the Nexus Events do in the regular timeline before they get reset.
I don't have immediate quotes on-hand at the moment, but in Episode 2, Loki and Miss Minutes discuss the whole reason they have to worry about Red Lining a branch, because it means that they can no longer reset it safely, as part of his training before the first Nexus Event he is brought to - where Loki himself attempts to stall until it red lines.
It's my understanding that the "Supreme Timeline" that He Who Remains and the TVA were in were subject to similar logic, as He Who Remains was speaking with the Lokis at his point in time on the Supreme Timeline. This meant that, as He Who Remains had not removed the Lokis who were able to start a Nexus Event where he lived, and nobody else was interfering with them to stop them from continuing on that branch, the TVA timeline began to Red Line at the moment that He Who Remains noticed he could no longer tell how the rest of the conversation was going to go.
While one could say that the moment he didn't know how the conversation was going to go was similar to how in Doctor Strange 1, The Ancient One could not see beyond their own death, that He Who Remains was not yet dead at that moment strikes me as him only knowing what happens until a timeline itself Red Lines, as the Nexus Evented Timeline Split has gone beyond what he wanted the timeline to be.
I think they should have just explained that there is the sacred timeline and all its branches that are loomed or woven into one ring from a begining to and end in a loop and the TVA exists in the space just outside but still connected and controlled to remain in its own time that runs in a different rhythm that allows it access to that sacred ring of timelines at anypoint within that ring they want to go or edit etc so that they can monitor it. All time is in this universe they are in is energy that is wound into a reality creating a stream and that stream needs to be monitored or it will just go wild and may hit other streams in the place they are in however the place where the castle is that he who remains is in was created outside the tva's timeline as well allowing he who remains to monitor its flow and he is within a timeline as well that he himself can control from within using his wrist device that Sylvie takes from him at the end after killing him.why they never bothered to search the place afterwards idk but thats what I think anyways at least it makes some sense to me . Like a pyramid with 3 levels the top controls the bottom two and the middle controls the bottom one simple right ? And as far as when Loki enters the second TVA crap well theres a reason we now know and that is that prior to Antman quantummania they planned on Kang first appearing there on loki season 2 in the begining and loki and the others fight and chase kang after different Kang in the 6 episodes and lose to some and win a few others but in the end the council of kangs gets rid of Kang the Conquerer after he tries to annihilate them all so he can rule alone with his own universe to himself without their involvement but they kick his butt into the quantum realm exiling his evil butt and that's where we would have seen him in Antman and it would have explained all this in that movie but it came out first because of the writers strike and setbacks it was easier for them this way.
