Alright. Let’s tackle this very confusing story, that I may have overthought. Here is my theory on the story of Evoland 2.
The original timeline does not begin with the Magi Era. The Magi Era is actually what came years after the year 1 049 (the future we see), which would make the years we travel into the Dark Ages that the Magi keep referring to. Something happened in the Dark Ages that made the Magis think there would be a Great Disaster and thus they created the Project to curve time so that they enter a loop and never get to the End of Time. They employ G to make sure the cycle never breaks. Once the Project is done, they activate it and lauch it into the Anomaly, then make Tiny Tiki (now grown super big), this creature that can create it’s own energy, swallow the Anomaly so that the Project never run out of power.
In my opinion, since the Sylph says that Kuro is one of the few that can chose his own destiny, I think something happened during one of the loops that made him forget everything. I think that in G’s first loop inside the cycle made him realise there was never a threat of a Great Disaster. That it was all a kid’s game. Learning this, he becomes professor Giro and tries to find a way to get back to the normal timeline. That’s when he learns about a young half-demon, half-human with great power. He goes in hibernation and waits for the second loop where he’ll wake up and wait for Subject X to come to him so he can build the Weapon and destroy Tiki, with the Anomaly and the Project inside.
In his second loop, since G is technically still alive, the Project needs to create a clone of G so that the cycle maintains itself. This new G has no memory of the first loop since he’s just a clone of the original G in the Project’s memory. Clone-G goes through the same things the original G went through, but when he gets to the lab with Fina, Giro wakes up and kills them both, leaving Sid alone in Windy Valley. When Subject X arrives to the lab, Giro captures her and starts the process in absorbing her power into the Weapon. When he loosens his grasp, she takes this opportunity and throws Giro into a portal. This portal brings Giro back in hibernation, with no memory of what happened, thus making him do the exact same things during each loop.
Since Giro killed Clone-G before he could finish his loop, G will now start his loop with no memories at all, thus creating Kuro. And that’s when we come in and play. Since the loop is now changed so that Giro, Clone-G and Kuro all start with no memory of what happened in the loop before, they can’t change what happens and they will forever stay in this cycle.
If you have any questions about the details, I have this huge file with the whole story I pieced together and I will happily share it with you if need be. If you have a theory of your own, please do share! This is one story that I’m not sure we’ll ever know the full truth unless the writers tell us.