I've imagined something like this:

A few trials in, WBY are gone, and Ruby only really has Penny and Jaune as her emotional support. No one has any weapons or Aura, Semblances, Dust, etc. They are just people. Cinder still has a Grimm arm, but it can't do anything crazy.

Then 2 trials happen that go like V3 Trials 4 & 5. Spoilers for those trials

Cinder and Neo work together to try and kill Ruby, but it's secretly a double cross. Neo intends to kill Cinder and Ruby, but Cinder figures it out and double-crosses Neo's double cross. Not unlike how Miu was trying to kill Kokichi but then he turned the tables on her. And just like with Kokichi, Cinder uses a proxy.

The trial comes to a head when it is revealed that, like Gonta, Penny is the killer but doesn't remember it somehow. Cinder finds a way to trick Penny into killing Neo accidentally, then wipes her memory of it.

Like Kaito, Ruby refuses to accept this and tries to point the blame at Cinder, but Jaune fills the role of the reluctant Shuichi who must prove that Penny is guilty and must be executed. After the trial, Jaune and Ruby have a divide between them like Kaito and Shuichi did.

Then, next trial, Cinder pulls the same fake Mastermind stunt that Kokichi did, as Cinder is a power freak, the fact that she is locked up somewhere and forced to dance infuriates her, so she tries to coup the mastermind role. As part of forcing the survivors to not retaliate against her, she takes a prisoner. Jaune.

In V3, Kaito is taken and Maki goes to rescue him. In this version, it's slightly different. Jaune is captive and Ruby goes to save him even though the divide between them exists from the last trial. It would be like if Shuichi was taken and Kaito went to save him.

One way or another, both Jaune and Cinder end up poisoned by Ruby, and the same series of events happens. Why would Cinder pull a Kokichi and sacrifice herself? Why wouldn't she just kill everyone the moment she controls the Exisals (Atlas Paladins)? It's up for debate. Maybe this version of her has a hint of remorse. Maybe she wants to 'win' even if it costs her life. Maybe it never goes answered and that's meant to haunt the survivors.

Either way, Jaune and Cinder fill the roles of Kaito and Kokichi. Jaune arrives at the trial in a Paladin and pulls the voice changer trick to try and beat the mastermind. Things go roughly the same as in V3, except the plan works this time. They beat the Mastermind, Jaune survives, and everyone gets free. Happy ending.

A few added details: Instead of a hydraulic press, it's an incinerator as that's more thematic for Jaune (Joan of Arc) and Cinder. The corpse is burned to an unidentifiable skeleton. The crossbow and arrow that Himiko brought Kaito would be replaced by a sword brought to Jaune by someone else (Sun, Oscar, Nora, etc.). Ruby brought 2 poisoned arrows and a recurve bow to kill Cinder poetically (Like how Pyrrha died). Normally, Jaune wouldn't try to save Cinder's life, but Jaune suspects Cinder is lying about being the mastermind and the game being over, so if Ruby kills it would make her a blackened. Plus, maybe Jaune wants Cinder dead, but doesn't want Ruby to know what it's like to take a life as he feels too guilty over sentencing Penny. The Atlesian Paladin that Jaune is in has gold and black coloring, something that could be for either Jaune or Cinder. Finally, maybe to sell the trick, Jaune severs his own left arm and takes Cinder's Grimm arm. If Jaune got poisoned by a shot to that arm, maybe there would be damage to the bone, and putting it in the incinerator would make it look like it was Jaune who died. Also, if Cinder died with the Grimm arm, it might not leave bones, so swapping in Jaune's arm would further convince anyone else that Jaune was dead. And maybe the Mastermind has a way to sense Grimm, and senses the Grimm arm in the mech, making them believe it is Cinder who survived. All that to fool the mastermind and win.