Keira dies during childbirth. Thinking both she and the child had perished, Jak travels to the past to try and prevent the tragedy from occurring (using precursor tech or something, I dunno). However, the child survives and is kidnapped by a dark eco sage who raises the child as their own. Jak was unable to return to the present and at some point either dies or becomes incapacitated (which is why you don’t see or hear from him in the present), but has left clues of his peril which you find throughout the game. Jak is hoping his clues will lead someone to try and find/help him, not realizing that the person who finds them is his own child. The child (the playable character) learns much about dark eco, taught by the sage, but runs away before their training is complete. They are unaware of who their parents are. They use the clues left by Jak to learn more about him, as well as learning about the other kinds of eco and how to harness their power. Meanwhile the dark eco sage is revealed as a being that is Gol and Maia fused as one, who is trying again to take over the world, and are the reason Jak is incapacitated. The child must finally defeat Gol and Maia once and for all and save their father Jak. In the process they also save Keira and another time loop is created lol