Sonic the Hedgehog and Jak 3 is set to premiere at an unknown date
Annie is now banished to the wasteland by a ploy of Count Veger and the city council. Sonic fears that Annie will die in the desert and goes to accompiny her and his friends follow him and almost died in the heat, though they end up being taken in by Damas and his wastelanders in Spargus City.
Jak accepts Damas' offer, and he and Daxter go through several intense objectives, such as battling giant Metal Heads in one of many dune buggies of Kleiver's in the desert. Pecker becomes an adviser to Damas and Sonic and the others go to Spargus school, where they befriended Vivian and Frankie and made new rivals, Jenna, Thrash and Terra. As Jak endures the heroic missions and the team doing school work, Sonic and Julie heared Felicia and Demon that they tricked the people of Haven City that Annie stoled their stuff and that they were the ones who stoled all of their stuff and Taylor just pretand that her necklace was stolen. Sonic and Julie sneak back to Haven City to tell everybody that it was the Black Widow who stoled all of their stuff. But they don't believe them until Darrienne showed up and attack Haven City. The Mayor of Haven City tells Sonic and Julie that Annie is now unbanished and they hurried back to the others to tell them that Annie can return to Haven City, including themselves. Jak refuses to go back due to his anger of Annie being banished, even when they mentioned that Haven City is overrun by Darrienne. He also meets a Precursor monk named Seem, who warns him of the planet's final fate being sealed by the Day Star (which is later revealed to be the Dark Maker Ship) as it approaches each day. After a few more missions, the team returns to Haven City through the Precursor Catacomb Subrails.
While in Haven City, Sonic and Jak are sent on missions into areas such as the Metal Head Section and the Sewers. At first, once Jak arrives in Haven City, he is cut off from the north section of the city by barriers set up by the KG Death Bots. The team must destroy the dividing barriers to reach the northern front (which holds Freedom HQ and New Haven City). He manages to blow the Metal Head section open by using his dark powers to destroy the barrier there. This links the Port with the Metal Head area. He manages to destroy the barriers in the Industrial Section by blowing them apart.
After opening the Power Station in the Industrial Section, Jak is sent on a mission to hack the Eco Grid there and retrieve a cypher key to decode the locks for the entrance to the KG War Factory. It is at the Power Station that they discover that Vin dumped his brain into the Eco Grid before he was killed in a Metal Head invasion. He helps Daxter retrieve the cypher from the grid. Once they decode the entrance codes, Jak destroys the defenses on the factory in an aerial attack with a HellCat Cruiser. He then enters the factory and destroys the factory's robot belt with the KG War Vehicle. He enters the control tower of the factory where he comes in contact with Erol. Erol is now Cyber Errol, after being severely injured in a Zoomer crash in the previous movie. He is remade into a cyborg form, with only half a face and a hand. Sonic and Jak battles Errol, who is backed up by KG Death Bots. After fighting, Errol flees the factory.
As the story progresses, the heroes encounter very strange and twisted creatures. They later learn after using the Astro-viewer in Haven Forest that these beings are Dark Makers. Jak learns that the Dark Makers were once Precursors, but succumbed to the exposure of Dark Eco, and in the process, became evil. What Jak discovers in the telescope is a Dark Maker spaceship, and it is proceeding towards the planet. Sonic, Jak and Daxter learn that the only way to rid the evil coming towards their planet is to activate the planetary defense system. But, there's a twist: the location of the planetary defense system is in the planet's core. And so after taking care of some Deathbots and Metal Heads, Jak and Daxter begin their trek to the Precursor Core. Sonic and the team have their friends in Haven City and Spargus to make a war to stop the invasion. Tails , Nicole and Woo the Wise remakes Big Green Base like a turtle so Big Green can both walk and shoot projectiles, hoping it will be enough to destroy the Dark Makers.
On their way, The team (Excluing Nancy, Nicole, Kiki, Dipper, Mabel, Susan and Mary) and Damas team up to fight their enemies, but their vehicle was overturned after being hit by a fire ball. Nicole saw it and she, Kiki, ApeTrully, Woo, and even Terra use the Big Green Base to fight Eradicus, but he shoots and destroys Big Green Base. Meanwhile, Sonic and his friends survived, but Damas is fatally wounded by being crushed under it. Before dying, Damas shows Jak the same pendant necklace that had been found on Jak's younger self in Sonic the Hedgehog and Jak II. Once Damas is gone, Jak realizes that he was his father. Darrianne reveals to Jak the truth and heads toward the planet's core and Sonic, Annie and Jak presses onward while Julie and the others go tell the people of Spargus that Damas is dead. As Julie and the others go back to Spargus, they meet a trio of Precursors. These Precursors, who after a trilogy of films were unknown, turn out to be Ottsels like Daxter. Julie sends Sonic, Annie and Jak to the Dark Maker ship to buy some time as the planetary defense system charges. The mission is a success, but not completely, for a giant spider-like mechanism piloted by Errol comes crashing down in the desert, and Sonic is forced to battle in one last fight. He spindashes off the legs, and then Errol ejects the top part of it and makes a last-ditch attempt to escape by flying away. But then he crash-lands just outside of Spargus. Sonic ascends to the peak of the remaining mechanism and subsequently destroys it. It is presumed that Errol is destroyed with the machine as its gas tanks (which were located right behind the cockpit) and uses his super form to defeat Errol and succeeded. The world is now saved and Narisa is the new Queen of Spargus. Commander ApeTrully then says it is time to rebuild Big Green. Nancy sees Sonic and runs after him until he lands at the sand close by Spargus. When Nancy stops running, she sees Sonic (back in his normal form) walking out of sandy wind towards her and tells her that it's finally over. Nancy runs over to Sonic and kisses him, which he does as well.
The story ends with Sonic with his friends and allies, celebrating their mighty victory against the evils that nearly destroyed the planet. The Precursors have the ability to change Daxter back, but instead Daxter just asks for pants, which he'd often talked about wanting throughout Sonic the Hedgehog and Jak II and Sonic the Hedgehog and Jak 3. After remembering who she really is, the Precursors grants Annie's wish by switching her and Tess' species, Annie turning into a normal Aura Whisperer Krimzon Girl and Tess turning into an Ottsel. Count Veger had also been turned into one, after asking the Precursors if he could be like them, without knowing at that point what it meant. Jak gives Julie his goggles as a thank you gift. The film ends with Jak revealing that his birth name was Mar, the same as the legendary warrior and Julie's childhood friend who she lost when she was 3 years old. The Precursors ask Jak to join them to see all of the universe and time. Once Jak leaves with the precursors, Sonic and the others rebuild Haven City having everything back to normal.
- First appearance of Terra, Jenna, Frankie, Thrash, Vivian, Phyliss, Wander, Sylvia, Lord Hater, Kayla, Narisa, Kristen, Benny, Selvaster, Megeran, Tim and Jill, The Mayor of Haven City and Annastagia the Hedgehog.
- This is the first time Terra has helped Sonic and his team.
- This is the second time an old person (Damas) helps Sonic and his friends, but leaves them. The first time an old person (Ma Bagge) helps Sonic and his friends, but leaves them (Actually she was pushed off the boat by Thomas) was in Sonic Unleashed (Cameron Version)