James Gunn has been busy building upon his work within the DCEU helming Peacemaker while also taking the time to dismiss Galactus fan theories as a part of his other life, the principal architect of the Marvel Cinematic Universe's cosmic arm. Shooting is already underway for the highly anticipated final film of his trilogy, Guardians of the Galaxy Vol. 3, which will promise to enhance the reach and weirdness of Marvel's teeming cast of characters. In addition to introducing Adam Warlock into the MCU, the film will also be featuring someone relatively new to the crew of the Benatar, a variant of Gamora from another timeline. Loki presented a brand new way to understand the multiverse, its various implications across fundamental elements of what is considered the Sacred Timeline and the ruthless way in which it is policed.
The current Loki of the MCU is Variant L1130 and he was charged by the Time Variance Authority (TVA) with sequence violation 7-20-89, a crime he committed while escaping from Avengers custody. According to Judge Renslayer it did not matter that Loki was the literal beneficiary of an Infinity Stone tumbling at his feet due to the actions of Earth's Mightiest Heroes or that his opportunity at freedom was in keeping with his nature. He was sentenced to being reset, a euphemism for banishment to the Void where he would be consumed by an entity conceived from the rips in space-time. Loki asserted his existence as a variant was because of the Avengers timeline heist and the same should hold true for Gamora, with the same judgment.
The TVA was built to reduce the multiverse into a single timeline in an effort to prevent variants of one specifically brilliant man from destroying or conquering all of existence, a man known so far only as He Who Remains, though one of his alternates is destined to become the MCU's Kang the Conqueror. The TVA pruned other variants that diverged from the Sacred Timeline and shunted off entire new realities all in the name of one glorious purpose, to make sure that Kang or another figure like him, did not come about to threaten existence. He Who Remains then orchestrated how reality should progress because relying on his omniscience, this was the only path he saw toward staving off annihilation. Much like Doctor Strange using the Time Stone in Avengers: Infinity War, He Who Remains peered into the potential outcomes and came away with one conclusion. The largest distinction between the two is that while Strange surveilled 14,000,605 futures, He Who Remains seems to have disposal to infinite timelines and came away with the TVA bureaucracy as the solution, to ensure that the desolation he witnessed during the Mulitversal War would not return.
He claimed his actions ended that war and protected the Sacred Timeline while he administered his will through his literal puppets, the Time Keepers. Through them the judges, hunters and other drones of the TVA kept the engine of Time spinning through the scripted choreography, staving off annihilation. Two Loki variants however united to solve the mystery of the TVA and ultimately discovered the man behind the curtain, but this too was another predetermined path designed to offer He Who Remains some respite. He offered them a choice, kill him and allow the multiverse to return in all its doomed glory, or take over and maintain the status quo that he had achieved. The variants disagreed, resulting in one of them killing the man at the End of Time and apparently unleashing Kang on the multiverse.
In the final scene of Loki's season one finalé the TVA is still functioning though it is besieged with timelines branching beyond their ability to control. Mobius and Hunter B-15 are seen trying to understand what "he" wants them to do before the camera pans to a statue of He Who Remains garbed in raiment reminiscent of Kang's comic book appearance. The alternate may be using the TVA to neuter potential threats before they manifest anywhere in the multiverse that he so desires while cultivating others for resources, alliances and the simple pleasures of future conquest. Gamora is an offshoot of the initial timeline in the same way that L1130 was, through no fault of her own and in keeping with her nature. There is a lot of narrative work to accomplish with Gamora as she bonds with her new old crew and thwarting the TVA's attempts to prune her would certainly complicate that but her return to the MCU in Endgame cannot be ignored given what the audience now knows about the inner workings of multiversal mechanics.
After Gamora of the prime reality was sacrificed by Thanos to secure the Soul Stone, she was replaced by a time displaced Gamora that chose to help Nebula defeat Thanos and save half of all life in the universe. This alternate Gamora may or may not have been part of He Who Remains original plan. He desired rest from his custodial duties to the timeline and the Lokis provided him with that chance and perhaps he had a similar plan in mind for the Daughter of Thanos. In either case the TVA would not be aware of those machinations. History has shown He Who Remains always kept his plans isolated from their purview, with the exception it would seem of Miss Minutes, the holographic companion fashioned as an orange anthropomorphic clock. In order for the timeline to flow naturally according to his coding of events the TVA goes about their business in ignorance of their true goals or of their true master. Considering that Doctor Strange in the Multiverse of Madness will prominently include a variant from introduced in a television property, and perhaps more than one, treading along this premise may be a matter of course by the time Guardians 3 releases.
Gamora would find herself subject to a reset declaration just as Loki did and if she did not have the benefit of some seemingly serendipitous intervention then she would be culled to the Void and await the oblivion promised by Alioth. Though both Kang and He Who Remains both seem to find a use for the TVA it is unclear at this point that they dictate identical mandates. Kang has distinguished himself as he eschews the need for figment intermediaries even though he seems to have left his lackeys with little information as to how to enact his agenda as the timelines reproduce exponentially. If they are following up their initial directive but are being overwhelmed by the amount of targets they must now consider, then she would be among them. Despite their interconnectedness the MCU shepherds have demurred when it comes to supporting the idea their properties work in collaboration with one another in a few notable instances, so Gunn may feel no compulsion to visit this area of Gamora's anachronism in any way, much less as it relates to the TVA. The precedent however has been established so Gamora's return to the big screen may include a visit from the sanctioned watchdogs of the Sacred Timeline.