WARNING: This article contains major spoilers for Loki episode 6.
By Avengers: Endgame. While Loki has worked to set up the future of the Marvel Cinematic Universe through Phase 4 and beyond, it has also tidied up details from the MCU’s history. One lesser expected revelation was that the Ancient One could be fundamentally wrong about how the universe worked.
The Ancient One was introduced as the custodian of the Time Stone, and then killed off in Loki took the MCU’s explanation of time travel to a whole new level as it explored the TVA and the creation of nexus events, and demonstrated that some people know more about timelines than the Ancient One.
The Ancient One explained that she cannot allow Banner to take the Time Stone from her timeline because the infinity stones control the flow of time. She continues, saying that removing a single stone from her timeline might save Banner’s, but it would cause her timeline to branch, and says: “without our chief weapon against the forces of darkness, our world will be overrun. Millions will suffer.” Loki demonstrates this to be incorrect, as in reality when a timeline branches the TVA arrives and quickly resets that branch of the timeline and it promptly ceases to exist.
While it could be argued that the Ancient One could be referring to Avengers: Infinity War,) she can see that if one were removed then time would stop for that reality.
However, this is not because the Infinity Stones create the flow of time, but because they are necessary for Kang’s Sacred Timeline to come to fruition. Any event that removed (and did not return) an Infinity Stone from the timeline would prevent Thanos from being able to use them in the snap and would stop Iron Man from being able to bring everybody back. Mobius (Owen Wilson) confirms in the first episode of Loki that this was part of the intended Sacred Timeline, and therefore the removal of the stones would cause the TVA to reset the timeline. It is entirely possible that outside of Kang’s plan the stones are really just powerful items and not actually necessary to the Universe’s functioning, which is why the TVA have so many that they can use them as paperweights.