Seven and-a-half years after the events of the first game, the protagonist receives a special mission from Elder Kai, which involves correcting history after it has changed. On the way there, they meet the Supreme Kai of Time, a deity who watches over time, and her bird, TokiToki. After meeting Elder Kai, they are granted their first mission, which is to correct Goku's battle with Raditz after he's been enhanced by dark magic. Meanwhile, Towa and Mira, the people who've caused history to change, have gathered allies, Turles, Lord Slug and a mysterious Masked Saiyan, later revealed to be Goku's father Bardock, from different parts of the timeline.
During the Attack of the Saiyans Saga, Turles attempts to intercept Goku to prevent him from assisting the Z Fighters against Nappa and Vegeta, only to be stopped by the combined forces of the Time Patroller and Goku. During the battle, Trunks and his partner, the protagonist from the first Xenoverse game, try to capture Turles, but he escapes before the Time Patroller can stop him. The protagonist then returns to the Time Nest after defeating Great Ape Nappa and Great Ape Vegeta, and correcting history. There, they are introduced to Trunks and his partner, and it is announced that TokiToki is laying an egg, which gives birth to another universe. During the Namek Saga, the Time Patroller helps Gohan and Krillin from escaping from Dodoria and Zarbon. After the battle Lord Slug appears and fights the Time Patroller. After the battle, the Time Patroller returns to the Time Nest only to find out that Captain Ginyu had switched bodies with Vegeta instead of Goku. The Time Patroller and Trunks attempt to fix this but in doing so, Ginyu switches bodies with Trunks. After the mishap, Ginyu finally switches bodies with Goku. (As part of the original timeline). After fighting the Ginyu possessed Goku, Ginyu returns to his body and attempts to switch bodies with the Time Patroller but Goku throws a Namekian frog in the beam, causing Ginyu to be a frog. The Time Patroller then must help Nail fight Frieza in order for Gohan and Krillin to obtain the dragonballs, causing Trunks to intervene and help Gohan and the Time Patroller fight.During Goku´s fight with Frieza,Cooler(Freiza´s Brother) arrives to help Frieza kill Goku,but is eventually defeated by the Time Patroller and Goku. Afterwards in the Androids era,Trunks tries to help Gohan defeat the Androids once and for all, but is stopped by the Time Patroller due to the Supreme Kai of Time stating that history would be changed. Because of this history, Trunks must take a break from time patrolling. The Time Patroller then travels to the Majin Buu era to fix the distortion in which Majin Vegeta sacrificed himself to defeat Majin Buu. Broly arrives, consumed by Towa's dark energy and attempts to kill Goku, Vegeta and Buu, but is stopped by the Time Patroller. Vegeta sacrifices himself to destroy Majin Buu, restoring the current flow of history. The Time Patroller then goes to the timeline where Goku and Vegeta defeat Kid Buu, learning that the Masked Saiyan is there collecting energy from the fighters. The Time Patroller chases after him and teleports to the era where Beerus and Goku are fighting. The Time Patroller defeats the Sayian, breaking his mask and revealing himself to be Bardock. Mira arrives and engages in battle with the Time Patroller. Beerus interrupts the battle with the intention to destroy Mira, Goku, the Time Patroller, and Earth. The Supreme Kai of Time tries to calm Beerus down with her pudding, but the horrible taste drives Beerus into a fit of rage, and he is subdued by Whis and the Time Patroller. Soon after, the Time Patroller travels to the Golden Frieza Saga, in which Frieza has been resurrected and wants revenge on Goku. During the battle, Cooler shows up again, consumed by dark energy and Frieza is consumed as well while in his Golden Form. Towa hacks into the Time Nest and tricks Beerus and Whis into leaving the battle, which allows Frieza to destroy the planet. Whis is able to rewind time and the Time Patroller, along with Goku and Vegeta, kill Cooler and Frieza.
Later, Beerus and Whis train the Time Patroller preparing him for the final battle with Towa and Mira. Trunks and the Time Patroller go to an unidentified timeline and battle the mind controlled Bardock. Mira arrives and battles the two, and Bardock is knocked back to his senses. He drags Mira into a time rift and both are supposedly disappeared. Towa then arrives and reveals that she has taken control of Trunks's partner. The Time Patroller and Trunks battle the two and retrieve the mask which Trunks's partner was wearing. Trunks's partner then vanishes from existence, leaving Trunks and the Time Patroller with no memory of him. The scrolls then pick up another distortion in time, causing Trunks to remember his partner and realizes that Towa went back in time to prevent Trunks from summoning him. The Time Patroller fixes this distortion and Trunks's partner is revived. Towa arrives at the Time Nest, and steals TokiToki's egg. Mira returns (Bardock defeats Mira as a Super Saiyan 3 but left him afterwards) and easily disposes of Trunks and his partner. The Time Patroller confronts Mira, who has become more powerful, finally gaining a fighting spirit because of his battle with Bardock. Towa realizes that Mira's power core is overheating, and would destroy the entire universe should it explode, and so she helps the Time Patroller defeat Mira. When Towa suggests fixing Mira's power core, he turns on her and absorbs her and the egg, gaining incredible power. Goku arrives and turns Super Saiyan Blue and helps the Time Patroller finally destroy Mira. With the universe saved, the Dragon Balls are used to summon a big feast for all of Conton City. The game ends with Goku suggesting that the Time Patroller and the Time Patroller from the first game fight each other to see who is stronger.