as I have been wanting to discuss this since the film went on sale as I bought a copy, now I am trying to avoid any major spoilers in the title this is going to be a three-part speculative discussion. So here are the three points I would like to discuss: how do you Darkseid turn batman, how far back do you feel barry needs to go to prevent the events of this film from happening, and what does he need to do to prevent it. (note: I am very long-winded when it comes to this kinda thing)
first, I would like to give off a bit of background in case you have not read up on them the paradooms are just as powerful as the Doomsday clone Darkseid sends to earth meaning just one is more then a match for the justice league and Darkseid has hundreds if not thousands of them by the start of this film. so by 2020 unless you have a massive hard of kryptonite like Lex Luther, Darkseid is unstoppable in conventional warfare as the paradooms can mow down all opposition and are completely loyal to Darkseid. I am stating this cause I got into a discussion about the second and third discussion points on DCFANdom/wiki and I do not think the guy I was arguing with realized this fact. link: Paradooms | DC Animated Movie Universe Wiki | Fandom
how do I think batman was turned: I think batman would rather die than allow himself to be reconditioned again. given that batman can out-think just about anyone in the universe you would want batman on your team. however, batman’s track record with contraceptives is nowhere near as good as his adopted son Dick Grayson, as there is the theory that Catwoman Helena kyle is not · Sam Bradley, Jr daughter but is actually bruces daughter, the theory put forth by the book Batman and Psychology: A Dark and Stormy Knight, then there are the various incarnations of Damian Wayne so batman is likely 2 for 2 with the only women he has been known for sure to have been interment with. well, Dick Grayson on the other hand is 0-wtfrk. given in hush bat and cat were going at it like bunnies I feel cat had a kitten on the way. Darkseid had several members of the league on his side by this time and would have likely been able to find out the relationship or already knew about it. given he wants batman on his side he likely would have planned to kill cat and Alfred to break the bat, however finding cat with a bun in the oven or a kitten, I would say he would have all the leverage he needed to get that bat to willingly submit to the reconditioning as the scout drone could have picked cat and kitten up.
batman craves a family more then anything else in the new earth continuity batman almost dies protecting Talia and his unborn child Talia faked a miscarriage and ‘divorced’ him to free him of that protectiveness. so yes batman sells his soul to the devil in a heartbeat to save the ones he loves. the deal his eternal loyalty to save the only women he loved and his children so cat, kitten, baby bat, and bird boy live. Given Damian went underground and dick likely having been killed well batman was being reconditioned as let’s face it even if he is willing it would still take time to fully reprogram batman. It also explains why Darkseid would keep the Paradooms close to home instead of just using them to conquer all before him. he realized they were a too blunt instrument that was hard to control when compared to his regular parademons. thus he uses the parademons to police earth instead of of the paradooms. and this theory is proven as the paradooms can not distinguish friend from foe during the final act of the film.
so Darkseid makes a deal he sends cat and kitten to a different eath in the multiverse and would wait for 100 to 1000 years to invade that multiverse and he would spare the baby bats. the reason bat was able to break from his willing reconditioning would be do to him subconsciously asking himself if he is worse then the man who murdered his parents as Joe Chill did not kill the one witness to his crime, thus he freed himself as Darkseid seemed shocked when bats threw the kryptonite katana at him. however, I would say he was willing to die for his betrayal of his dark master as batman has been able to avoid Darkseid’s omega beams in other continuity well in this film batman did not even try to avoid the omega beams he just stood there ready to take the hit. then Damian willingly gave his life for his father. also, the cat was not shown to be with the bat family nor a part of the second invasion of Apokolips. let’s face it even though she left him if cat new bat was turned she would move heaven and earth to bring bat back to her. I will admit so I am giving her absence a happy ending as Darkseid is ruthless enough to just kill cat and kitten in front of bat to break him, but he is also smart and clever enough to not rely solely on brute force to get his way. I also spent quite a bit of time thinking and likely overthinking cats’ absence in the film.
my answer to the second and third questions are fortunately much, much shorter: Barry simply has to go back to the time justice league war, and prevent supermans capture or remove all data of superman DNA, all and all physical samples of superman DNA that may have been collected… however, the time quake would cause some changes to the timeline the biggest being no death of superman…or better yet a better adaptation of the death of superman with a not Kryptonian doomsday.
as to cyborg as a sleeper agent, we viewed from the forth wall know cyborg was a spy but it is unknown if the rest of the group ever new that he cyborg was the ultimate spy.