Here is my theory of what could happen after the ending (after launching the Ark and Simon-3 is left alone behind and Catherine's chip breaks).
Simon-3 heads back for Theta, in order to find the first Ark prototype (where he did the Dummy simulation for Catherine). He is determined to make a new scan and get aboard that ark, which he can design as he wishes before jumping in. He chooses to recreate his past life, and populate it with scans found within cortex chips and the legacy scans in the Theta computer (one of them is Dr. Munshi). To be sure he will not fail this time, he will try Sarang's continuity theory to "cheat" the coin toss (he will set the suit's battery to drain or overload immediatly after the scan is made).
After he leaves the space gun site, he takes the elevator out of the abyss (with the cortex chip fried, the default "Helper Jane" AI gets back online and he uses an Administrator console at site Alpha to get full security clearance (Administrator Mode) to open all doors). at Omicron, upon entering through the suit bay airlock, he will face Simon-2.
Technically, Simon-2 never actually dies, regardless the choice in the game! Draining his power cell will only put him into some sort of stasis, and when the cell is recharged or replaced with a new one he will wake up! It is just like unplugging and then plugging the Omnitoole with Catherine into a console works, she does not die, but the time passes instantly for her, with gaps during the times she was unplugged. The same happens for Simon-2!
Simon-3 can choose to recharge Simon-2's cell and revive him, if he does so they could have a philosophycal discussion about existence
... Don't know what to do with Simon-2 though...he could go mad learning that there are two of him and that the Ark was launched without him and attack Simon-3, and be defeated by him...Or they could go along together until at some point there is an accident and he sacrifices his life to save the player (Simon-3).
Then Simon-3 heads to the Structure Gel labs at Omicron, where he previously used the lab station experiment to fix the chip and revive the dead rat. He pours and activates Structure Gel over Catherine's broken Cortex Chip, bringing her back to life!
They use the shuttle to get back to Theta, where the revived Catherine helps Simon-3 reprogram the original Ark prototype. He recreates his old life, Toronto, he places Dr. Munshi and uses the other scans found in the database to make new AI-s, putting their personality in simulated bodies of his friends or relatives. He even creates a simulated body for his dead girlfriend Ashley, but he has no scan to use for her personality.
He powers the new Ark, ensuring it enough backup power to last for at least a thousand years, locks it safe in the lab, barricading the doors and using pneumatic seals on the doors and proceeds to scan himself. Before the scan he sets his cell pack to explode immediatly after the scan, in a desperate attempt to cheat the coin toss, like Sarang and the others did.
As he is scanned, Catherine says she will not leave him alone, she will come with him. The scan is finished and the scene ends in a white flash / explosion.
Simon awakens back in Dr. Munshi's lab, after the first brain scan (back in 2015). He tells him that all brain damage has miraculously dissapeared, he is perfectly healthy. Upon leaving the lab, Ashley, his girlfriend awaits him. He asks amased something like "But how is this possible?" She replies "What are you talking about honey, let's go home." (Catherine put her scan in her body so she could be with Simon).
Simon: "Maybe it was all just a weird dream"