Many years after defeating the metal head leader Jak and Daxter had made lives of there own. Jak was married to Kiera and had a child named Kent. Daxter was a video game champion of the city and was awarded by king Jak the City wide Video game award. They basically had settled down in the world for the first time and were relaxed with the lives they had.
One day though the city had had an earthquake and many buildings had collapsed causing several casualties. Jak went to honor there deaths at a city wide funeral when it happened, When announcing the casualties there was a loud BOOM! In the middle of the crowed a metal head ship had crashed and metal heads were spilling out of the hatch. Jak turned to Kiera and told her to take Kent and go to the underground base with Kor. After that Jak did a front flip off the stage and ran right into the middle of the metal head attack. Jak had no weapons, but that didn't stop him from fighting. A crimson guard threw him and electric shock gun, Jak started by shooting a small metal head at his feet, followed by a shot to a metal head's head. After fighting for thirty minutes Jak had defeated the metal heads and returned to the underground to see Keira, but was horrified when he found out what happened. Keira, Kent, Torn, and Samos were all kidnapped, Ashlin the Barons daughter was the only one left, and she had informed him that the city was breached and that all of the citizens were thrown into metal head prisons. Ashlin was crying at the fact that her lover Torn was taken by the metal heads and was swearing left and right as tears of rage and hate poured down her face. Jak to felt sorrow as his son, wife, friend, and father in law was kidnapped by the species he hates. But then he heard a voice from under one of the bunk beds in the underground base that he recognized and loved, Daxter. Daxter was cowering under the bed when Jak threw the bad out of the way, when he did this Daxter yelled "Aww"! He began to scratch and throw punches without looking, until Jak said "Dax come down its me Jak". Dax stopped immediately and jumped on Jak and started to kiss him all over the head, "you tell anyone I ever did that, and you are dead sista" Jak laughed with a relief that his best friend was still there and he was alive. Jak asked Daxter if he was ready for another trip to the metal head nest, Daxter replied "No, never, why, ok". Jak accompanied by Daxter and Ashlin walked into his room, he reached under his bed and pulled out a suitcase, he opened it and just stared at it for the longest time. The blue tunic, brown boots, and all of the guns; and gun upgrades lying with it. "I never wanted to look at these again but if they are going to push me then I will push back". Jak pulled Daxter onto his back and handed him the scatter gun, Jak gave Ashlin the key to the gun fortress and told her to guard the tomb of Mar as the precursor stone was there. Jak climbed pulled out one more things out of the suitcase, the hover board Kiera gave him long ago. He climbed on it and headed for Haven forest. Daxter held the scatter gun in his hand blowing up the occasional metal head. When Jak and Daxter reached the entrance to Haven forest, there was much sign of struggle as blood had stained the pathway up to the doorway. Jak entered through the first door as the second began to open, the sounds of rusty hinges and cranks were louder then ten years ago. When Jak saw Haven forest he could not believe his eyes, metal head nests everywhere, no sign that there was ever a forest there. As he took a step forward he ran right into a wall that could not be seen, the wall was in fact not a wall but a metal head that had a cloaking devise on. Jak pulled out his blaster before the metal head could react and shot him right in his glowing yellow jewel. Jak reloaded his blaster and then set off down a path to the heart of the nests; it wasn't long before Jak was shooting everything in sight. It was chaos, while Jak was shooting five metal heads while Daxter was blowing away metal heads with his scatter gun. After a long time of fighting, Jak and Daxter gave up on trying to individually killing them, Jak pulled out the peace maker and shot one shot and destroyed all metal heads in sight. As Jak went into the big nest in the center, he noticed something that caught his eyes. The path leading further into the forest had two dead guards lying on each side of the entrance into the path. Jak got on his hover board and skated over there to see what it was, when he heard screams for help. The screams for help grew louder and louder as Jak got nearer, when he reached the entrance to the path he realized that it was were the prisons were. He turned the corner and realized then that it wasn't a prison it was a dungeon for torturing. Jak broke did a spin on the hover board to get a boost of speed and chased the screams as fast as he could. Then before he could reach the screams five metal heads had emerged in front of him from the ground. Jak pulled out his Blaster, but noticed something when he reached for it, they had Kiera. There was something odd about this, how would mindless metal heads know that he was after Kiera. He took out his Blaster and shot the metal heads before they could react. Jak ran to Kiera's side and picked her up, she looked beat up, dirty, she was bound at the feet, hands, and was gagged by a rag. Jak removed the rag and asked her if she was ok, but something odd happened when he did this, her wait began to get heavier, her skin began to split, and before he knew it the metal head leader was right in front of him. Jak felt despair, confusion, and most of all, he felt hate. And right as he felt this, he felt a feeling that he hasn't felt in the longest time. His eyes turned black, his skin went dark blue, his fingernails grew into claws, and horns grew from his forehead. Dark Jak had returned and just as he did this the metal head leader changed into thousands of tiny scorpion like metal heads. Dark Jak did not hesitate to use one of his dark powers he learned; he jumped up and landed with a Dark Bomb causing all of the metal heads around him to immediately dissolve. Dark Jak began to run towards the screams feeling the hate and rage starting to get even larger. As he was getting closer to the screams his horns began to grow larger and his claws sharper. As Jak's Dark powers were increasing he felt inside the control decreasing. His mind was gone but his spirit remained, everything was on the line now, his people suffering, his child imprisoned, and worst of the metal heads were responsible for it all. Jak even started to hear a new voice in his head, one of hatred, sarcasm, and evil.
When Dark Jak had finally reached the torture chambers his mind was so lost that he didn't even remember what he was doing. The torture chamber was in a cave, the floor was moist but hard, the walls lit up by yellow metal head jewels, and all of the citizens of the city were in chambers that went as far as the eye could see. Dark Jak was starting to get angrier and as it got angrier, his horns grew longer, his claws sharper, and his heart turned black. The smell of death had made him even angrier, all of this hatred and darkness was building up so much that surly he couldn't return back to his normal stage of life, but I stand corrected as Dark Jak's powers vanished as easily as they had emerged by one voice. "Snap out of it Jak" the annoying hi pitched voice awoke Jak out of his trance of hatred, it was Daxter. "You think that when I fell off your back at that fight with those metal heads you would have returned to your best friend", "Dax" Jak stumbled it felt as if a load of 100 pound weights had been lifted from him. "What happened"? asked Jak catching his breath, "you were big bad and blue all over again, what's happening to you buddy" said Dax in a concerned voice that Jak had never heard from Daxter's mouth. "He's back said Jak, he is taking over me" Jak dropped to his knees wiped of all energy. Then a voice came from one of the sells in the torture chamber, Jak opened his ears trying his hardest to hear it again, "Jak" Jak broke into an immediate sprint. When he arrived at the voice he saw Keira and Kent at the bars of the chamber yelling Jak's name. Jak tried to pull open the gate to the chamber but was impenetrable. Jak thought of what could open the doors when it popped into his head, the only one that could tear this gate out was Dark Jak. He began to collect all anger he had and focusing it on the gate but just the relief of finding his family brought so much happiness that he could not change, but then something happened, the love and care for his family brought something new into Jak, his skin turned blinding white, his eyes a piercing yellow, his horns appearing to be tamed and going back to the curvature of his head, his claws were sharp yet trimmed, this was a whole new Jak. When Jak realized what he was, he went to pull the gate off, with ease and no stress the gate slid off its hinges. Keira and Kent had walked out of the sell, White Jak told his family to take Daxter and get out. when they left he jumped in the air and like a bomb hit the ground, the cave floor shook, a ripple of impact traveling at a high speed knocked all of the gates of there hinges. The citizen of his city walked slowly and fearfully out of there sells as if expecting something to happen to them. White Jak said "Jak I will return when the Dark one does" Jak began to morph back into himself; the people loosened up after this and even began to socialize. Jak told the crowed quiet down and go to the underground base were they would be safe. As for him he was taking the fight to the main metal head nest.

Jak traveled day searching each metal head nests, people at the underground began to get anxious, Daxter however though that Jak was just fine and that there was no need to worry. But after a week even Daxter began to worry about what was happening to Jak.
As the days past Jak grew more frustrated as he could not find were the metal head leader was. He checked every nest there was to check; he even went through the trouble of terminating all of the metal heads in there nests.
All seemed hopeless, maybe the attack was just a last chance attack, and maybe there was no metal head leader. After thinking on this awhile Jak just got up and headed towards the entrance to Haven forest, but right as he got to the entrance he felt a knife go into his back, he looked behind him in pure shock, the metal head leader stand there looking more vicious then ever, Jak fell to the ground weak and unable to do anything as the stab had paralyzed him, the metal head leader picked up a soared as if to stab Jak but right as he did so the hate and rage rose up in Jak, he went completely dark and then something that has never happened before, Dark Jak leapt from Jak's body and jumped into the metal head leader. The metal head leader began to fall apart, arms fell off, tentacles rapped themselves around himself suffocating the metal head leader, Jak was relieved of hatred and everything else but then the unthinkable happened, Dark Jak leapt from the metal heads torn body and took its soared, he walked to Jak and jumped in the air, for seconds Jak was confused but then there was no time to think, Dark Jak landed with a bomb knocking Jak out.
Jak woke up in the outer city, hanging from his hands over a sea of metal head scorpions.