The 2nd season of BoBoiBoy begins with his return to Rintis Island and his first day at school. There, BoBoiBoy starts to meet many new friends, not to mention the closest to him; Gopal, Yaya, Ying and Ochobot.
An ecstatic Gopal starts to tell several urban legends of the hanted house that's along BoBoiBoy's path that he uses to go back and forth to school. Little did they know, the house is owned by one of their classmate who just moved to the Rintis Island. BoBoiBoy doesn't believe in the ghost stories challenges Gopal to visit the house and inbestigate the matters so he doesn't use a much longer path to school.
As this happens, an excited Probe tells the story of the haunted house to Adu Du with the hope that they can ally themselves with the ghost to defeat BoBoiBoy. Who is this ghost that is being chased by them?
During one of the P.E classes PapaZola, who now works as a teacher has decided to hold an egg and spoon race. Even so, BoBoiboy and his friends deemed the race too childish, but gets all excited after PapaZola presents the prize for the winner; a PapaZola 'P' Ruler. This has build their interesting in the race, especially between BoBoiBoy and Fang. The race starts to get interesting as both decide to use their powers to defeat each other…
PapaZola disagrees with the usage of super powers and makes another match; a 5 on 5 football match between Fang and BoBoiBoy's team. The rule is that both can't use their powers and it has to be fair. BoBoiBoy manages to get his best friends to agree to fight with him, but what about Fang? Who will Fang team up with? How can they win this match if both can't even use their powers?
BoBoiBoy is helping Tok Aba up at the Cocoa stall early in the morning to find out who is the person who has bought all of Yaya's cookies. Apparently, it is Fang. In the same time, Adu Du gets an idea on how to defeat BoBoiBoy. BoBoiBoy and Gopal quietly follows Fang into the Cowboy Senin Alley and had to run away from the terrifying Crazy Cat. They now know the true use of Yaya's cookies. Probe suddenly appears and shoots them with the Shrinking Blaster.
BoBoiBoy, Gopal and Fang has now become tiny and has to find a way to get to Tok Aba's Cocoa stall where they can ask for Ying and Yaya's help. Adu Du and Probe celebrates their win after Computer informs them that BoBoiBoy will soon shrink until they vanish from this earth. The three now has to go through Cowboy Senin's alley and fight against the terrifying Crazy Cat. Can they defeat the Crazy Cat and return back to normal?
BoBoiBoy and friends are concerned with Ochobot's situation who is always shocked by an electric jolt when he sees Fang. This creates tension and assumptions between them. While this happens, Adu Du and Probe is still trying to plan a way to defeat BoBoiBoy. They are confient they can win with the new Emotive Chemical Y.
After they were ambushed by Adu Du who blasts them with the chemical, BoBoiBoy and friends starts to react strangely after feeling the effects of it. They struggle their way to Adu Du's Boxy Bunker to return themselves to normal, and also find out the truth between Fang and Ochobot. Has Fang been working with Adu Du after all this time? How did Fang gets his powers from Ochobot?
Adu Du uses his Recycled Tiger but still finds himself defeated by BoBoiboy. He decides to sabotages the Rintis Island's TV broadcast out of anger and disappointment, and screens their propaganda video; Adu Du and Probe in the morning. Adu Du makes up stories about the 'evil' BoBoiBoy with his plan to fool the people of the island.
Meanwhile in space Ejo Jo is getting nearer to earth and manages to locate Adu Du on the planet. He comes complete with his own Destroyer Robots and knowledge of the true power of BoBoiBoy and his friends. Who is this Ejo Jo and is he one of Adu Du's allies? Can BoBoiBoy defeat Ejo Jo?
It's now exam week! BoBoiBoy and his gang are studying hard to prepare for their Mathematics exam. Worst is Yaya and Ying who are always at loggerheads with one another during each exam week!
Meanwhile, Adu Du and Probe attempts to disrupt BoBoiBoy and his friends during their math examination but Ejo Jo's sudden arrival threw a wrench into both sides' plans.
Armed with the Destroyer Robot PeTai, Ejo Jo successfully managed to eliminate Probe and focus his attention on BoBoiBoy and the others. How could they defeat Ejo Jo who has already known the weakness of their powers!?