A/N: This is the original story outline. Read it and find out how it has changed from the original idea.
When Jak entered the time machine at the end of Jak III he is told that he will get to see the universe. The precursors take him back in time to the time of Mar giving him a sealed box which won't open untill he needs it's contents.
Meanwhile Mar who is a young warrior is fighting in the metalhead wars. Jak arrives and sees Mar fighting metalheads in the newly established Haven city (which is still primitive and based around Sandover village) and decides to help out. After they have beaten the metalheads back from the city Jak has a flashback to how Sandover is looking in the future and tries to warn Mar. Mar doesn't listen and continues to go on with his daily life. Eventually a giant metalhead (kors mother)arrives and destroys sandover.
Jak and Mar fight the beast and eventually manage to wound it enough for it to back off but before it does it fires some sort of poison missile at Jak. Mar dives infront of it saving Jak but ensuring his death. Mar is able to apologise to Jak for not trusting him and then tells Jak to protect the people and not let them find out of his death.
Jak returns to Haven and box the precursors gave him opens. It contains Vin who helps Jak fool the people into thinking that Jak is Mar. Jak spends most of the next 20 years protecting Haven and Mars family also slowly building up haven city. Then Jak tired of the metalhead attacks heads to the cave where Kor was in Jak 2 and figures the only way to protect Haven for long enough would be to seal the cave which he heads off to do making a big thing of it so that all the people would know that he was gone. he gives the disc with Vin on it to Mars son (who keeps it as his adviser untill the disc finally runs out of power years later and turns it into the amulet of Mar)
Jak heads to the metalhead cave and finds not kors mother but one of the precursors that bought him to this time. The precursor tells Jak that he can go home now and that Jak would be cured of his weariness when he is sent back (or forward in this case) to his own time.