What's missing from The Flux story is The Master. At the heart of this story is The Doctor's history as The Timeless Child, a tidbit uncovered by The Master who told this to The Doctor. So, that makes The Master part of this story, but where is The Master? How could there be a cockamamie universe-ending plot without The Master being involved?
If the Flux Story needs The Master to be present, who would it be, and where is The Master? There is a person in this story, The Great Serpent, that is almost certainly The Master.
When we first met The Great Serpent, as a life memory from Vinder, it was clear this guy is very evil. He, however, could have been a throwaway character, one that helped form Vinder's life. But, we see The Serpent returning, on Earth, concocting an evil plan.
Namely, he ingratiated himself with the General who was assigned the task of launching UNIT. The moment shown here is in 1967, shortly after the events at The Radio Tower (reference to The War Machines, a 1st Doctor episode). Additionally, the TARDIS was in his office, because it had been found in a village in Devon where everyone had disappeared. That would be the village that The Angels had attacked in the previous episode.
The critical point came in 2017. By that time The Serpent had been in charge of UNIT for 20+ years.
During the previous season I noted a probability that The Master had killed UNIT: Did The Master kill UNIT in Doctor Who Season 11?
During Season 11, The Doctor faced something which required UNIT intervention. She tried calling the UNIT hotline only to learn that it had been shut down due to budget junk. During Season 12, the Spyfall episodes, we learn that MI-6 had taken over issues regarding The Unknown, or what had previously been UNIT's job. Further, that The Master had infiltrated MI-6. And further that there had been a series of mysterious deaths of spy agency operatives. It seemed that The Master wanted to degrade the Earth's capability of detecting extraterrestrial threats.
We now see The Serpent taking over UNIT, and then in 2017 shutting it down. While doing so, he tried to kill Kate Stewart, but she escaped, and "went dark". The Next Time trailer shows her, of course, as some kind of leader of Earth's Resistance.
During Season 12, we did not know why The Master did all that. But in this episode we see a culmination of a plan, in which The Serpent (a.k.a. The Master?) was making a deal with the Sontaran Empire for them to take over The Earth. The deal involved negating the Lupari shield, so that Sontaran craft can teleport themselves into position above The Earth, and launch an invasion.
Does this mean The Master knew about The Flux ahead of time? When the Sontarans described having people who could predict timelines, and possessing time travel, we should have gone "hey, wait a minute". I'm pretty certain that Sontarans did not previously have time travel, nor would they be likely to have time sensitives in their staff. In other words, The Master could have given them technology like this, in exchange for a plan of the Master's devising.
Clearly if UNIT were still in existence, the Sontarans would have had a harder time taking over. Therefore, UNIT was shut down to enable The Sontarans to conduct their plan. But that doesn't seem very Sontaran-like, does it?
This whole plan smells like The Master.
As for The Serpent.... In the 1996 television movie version of Doctor Who, we saw a form for The Master which was a serpent which ate other bodies.
It's not the first time that The Master had occupied someone else's body during a period in which The Master did not have his own body. The Master's last appearance, on Gallifrey, at the head of what would have been an army of Cyber-Time-Lords built out of the bodies of The Time Lords, that ended with a big bang that was supposed to wipe out all life on Gallifrey.
That means The Master was destroyed? Not likely. The Doctor needs his/her Moriarity, and The Master always survives.