In the end, with Leon's help, Jake obtained the powers of the enemy and used them to create a place the humans from his universe could live. A shit ton of mana was used to create a place that resembled their previous home, but Jake had the means to gather all that mana with the traits that he had.
Bringing back to life all of those people that died during the assimilation was kind of easy once Jake passed to their memories a part of the traits that he absorbed. Thanks to that, they also all knew what had happened in their previous life, and now they knew that they couldn't make the same mistakes…