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This is actually a great question and there is a big foreshadowing in '' Happiness 1'' regarding it that seems everyone missed it.

The theory the series follows is the ''multiverse theory''  ( every choice you make has its own timeline)

So Future Alex created the TSR version 1 in the future ( a device able to only transfer you to the timeline the SEED of the time branches exist in)

Meanwhile, the Butterfly created the TSR version 2 ( a better device able to transfer you to any timeline you want )

Future Alex noticed that the Butterfly was deleting time branches and set a mission for himself to stop him but Butterfly killed him. Mirall found future Alex's body and vowed to finish his mission to stop Butterfly.

Then the events of ''Happiness 1'' happened and all timelines were destroyed. 

Alex fell on his knees and begged for a chance to re-create the timelines and to save his daughter. The ''SYSTEM'' listened to his plead and Alex became the new God of time.

Because of these events, Alex was sent into a different timeline ( a timeline where he defeated butterfly and met Mirall when he was a teen)

So basically we are now in a completely different timeline than the one where Alex creates TSR version 1 and are killed by Butterfly.

But that said Alex says something important in ''Happiness 1'', exactly in the beach scene with Mirall. 

Mirall says she will go to the future and kills Butterfly before he murders future Alex but he tells her that you can't defeat destiny and what's fated to happen will happen and no matter what you do the dead will stay dead.

This was a big foreshadowing that the series will end with Alex's death and that ever since the events of ''Happiness 1'' he was a dead man living on borrowed time granted to him by the ''SYSTEM''.