Speed Racer Sr. finally returns and reunites with his sons, however X is angry with him. The Mach 6 is stolen by Zile, and the Racer family works together to retrieve it and get Zile arrested. After getting back the Mach 6, Conor discovers a mysterious energy signal coming from the Mach 6, forcing the gang to investigate.

School is back in session at the Academy. However, the Mach 6 starts to exhibit new capabilities during a race.

Speed and his friends are attacked by the shadow committee. When they start to believe that Zile is somehow responsible, Annalise helps X and Speed get into the prison to question him about the attack. Meanwhile, Jared and Jesse spy on Speed and the gang for the Shadowy Woman and the Committee.

Speed and his pals must work with Annalise in class, but they have doubts about whether she's trustworthy. Annalise soon warms up to the group, but when it is time for the final team race, the Shadowy Woman contacts her and orders her to make sure that Speed and the Mach 6 are sabotaged by one of the men during the race. However despite the Shadowy Woman's threats, Annalise takes the hit for Speed instead but loses her car in the process.

The students are forced to mix up and swap cars. When another student, Mitch drives Jared and Jesse's car, he receives a message from the Shadowy Woman to get the Mach 6 files and decides to steal them for himself. Meanwhile, Speed and Conor go into the virtual track to find out how the attackers from the team race got into it and find that the attackers manage to create a tear allowing them complete access.

Speed and the gang go to Spritle to tell him about the tear in the virtual track. However, this causes Spritle to shut down the track for a week until it can be repaired. When Speed Racer Sr. warns the gang about the Alpha Academy, Speed and his pals investigate the school. Are they up to something? Meanwhile, Speed figures out that one of the Alpha students somehow managed to steal Annalise's car.

Spritle hires a new security team for the Racer Academy and Speed doesn't trust them. They soon figure out that the security team works for the Shadow Committee and is trying to get the Mach 6 files scanned. Later after recovering the disk, the gang checks to see if they got the right one, only to uncover a new missing piece of the Mach 6 shaped like an hourglass.

While Conor experiments to try to find the missing part to the Mach 6, he accidentally opens up a time vortex! While the gang tries everything they can, Conor finally figures out a way to close it. Speed must "jump" through the vortex to go into the past. Past Conor doesn't remember a thing, but Speed plays a DVD of "Future" Conor, saying that they must not experiment for the part anymore and that Tuesday is Taco day. Speed and Conor both realize that they must now hunt down the missing part before it gets into the wrong hands.

When the crew receives a contact from Speed Sr., Speed assumes that his father needs their help at the Alpha Academy, so he, X, and Annalise go undercover and sneak into the school to find him. While X gets into trouble with Headmaster Moustache, Speed and Annalise find a secret lab at the bottom of the school only to be caught by Speed Sr., who was actually undercover the whole time and only meant to send the message telling Speed and the gang to stay away from the school. He tells them about the Shadow Committee and how they are trying to make their own version of the Mach 6's missing part though he is not sure why.