BoBoiBoy Pioneers moves back to the island to live with his grandfather, Tok Aba and his friends after being apart for six months (end of the first season). In addition, BoBoiBoy has also been moved to another school, where he remeets and becomes classmates with his old friends, even having Papa Zola as their Mathematics teacher.

At Tok Aba's Kokotiam, Kumar (Gopal's father) tells Tok Aba and the rest of the customers about the haunted house for several hours. It spurs BoBoiBoy to investigate more deeply about the house, asking Gopal to help film the 'ghost'. Probe is also interested in the ghost house and tells his boss, Adu Du, to go there to woo the 'ghost' to be a member of their team.

Papa Zola teaches physical education classes, and challenging for race BoBoiBoy and Fang took the egg in a spoon as a way to discipline those who consider sport 'childish' and 'challenging'. Both opponents compete fiercely on the track and had to use their super powers just to beat each other, with a special Ruler P from Papa Zola as the prize, but the race ended with an unexpected result as Papa Zola win the race, and causes dissatisfaction from Fang.

As arranged the previous week, BoBoiBoy with Gopal, Yaya, Ying and Iwan worked together as a team in a football game. While Fang also worked with Adu Du and Probe as another opponent to beat BoBoiBoy in the game. With this, Mr. Papa Fair (who is just Papa Zola) became a referee in the match.

BoBoiBoy and Gopal began investigating why Ochobot fainted at the sight of Fang and why buy Yaya's biscuits every day before going to school. As a result, they were attacked by a crazy cat (Sewell cat), a cat protection Pak Monday Westerns. Therefore, they tried to escape and they finally pass one second to go to school. To go in the classroom, BoBoiBoy sneak into the staff room to avoid Yaya, the watchdog said that keeping the school gates. However, they are interrupted by the name and the image appearing in the Wall Yaya success.

In small delicate situation due Pistol Attenuator Adu Du, BoBoiBoy, Gopal and Fang quickly tried to go to the Tok Aba store to find Yaya and Ying to against their enemies. However, they must go through Lorong Pak Monday Westerns was dominated by the crazy cats, then Fang suggested that they bring biscuits once there to beat the cat. After that, Yaya and Ying took them to Adu Du's box headquarters to find a cure. After returning to their normal sizes, BoBoiBoy begin to ask Fang why Ochobot fainted when see his face.

BoBoiBoy asked Fang why Ochobot fainted every time sees his face, but Fang could not answer for sure. After hearing the proposal Probe on recycling old ideas, Adu Du repair and renew Liquid Emotions X from last season to Pistol Emotions Y is used to invert the five enemy character.

BoBoiBoy, Ying, Yaya, Gopal and Fang turned their peculiar temperament of Emotion Pistol Y marched to the headquarters of Adu Du to find a cure for Creative Ochobot. At the headquarters, the five of them are faced with a thousand and one traps set by Adu Du and Probe, while Ochobot and Fang gradually return considering how Fang gained power and also causes fainting Ochobot every time she saw the face of Fang; after that, Fang impact on Ochobot eventually fade.

BoBoiBoy and friends finally seized the antidote from Adu Du and defeat the enemy with Tiger cycle easily. BoBoiBoy also apologized to the suspicion Fang. Once again disappointed with the defeat, Adu Du and Probe plans to seize the wave of television broadcast called MKHIPI or Markas Kotak Hari Ini Pagi Ini for airing interviews with intent to defame BoBoiBoy for any errors the young hero created by him, including also invited Papa Zola. However, their plan was not so into as only 5 people watching.

Adu Du was surprised to learn that Ejo Jo knew about the mission on Earth. Adu Du tried to warn him about BoBoiBoy and friends but Ejo Jo insists on coming to Earth, says that he is really ready to fight.

Mr Papa Zola has announced that there will be occupied Mathematics exam student after the break. And BoBoiBoy also get to know about the best student battle between Ying & Yaya. Adu Du to know about it through the Probe was posing as a student and entering 5th grade honest. Although BoBoiBoy and others have criticized Adu Du and began to teach him, Mr Papa Zola prohibit them from doing so and Adu Du was accepted as a new student in the class. When the examination is underway Mathematics, Adu Du destabilize the situation by using the weather machine. Suddenly, Adu Du surprised to find the weather becomes cloudy, whereas he never ordered it. Apparently, the spacecraft Ejo Jo had arrived and landed on the roof of the school BoBoiBoy.

BoBoiBoy, Yaya Ying, Gopal and Fang and classmates face to face with Ejo Jo for the first time. See Probe knowledging him as a combat robot, make Ejo Jo felt funny. Therefore, Ejo Jo directing minions to reduce its combat robot, P.E.T.A.I. to show the real face of combat robot to probe. Then, P.E.T.A.I. dabertarung start an all-out attack by Probe. Using Super Probe, Probe can survive until ... Probe maintain Adu Du from being shot by P.E.T.A.I .. As a result, Probe died in the bosom of his own master. While teachers and classmates BoBoiBoy (except Fang) was captured and taken prisoner. Unable to do anything, BoBoiBoy and Fang were forced to retreat first.

In order to save their friends, BoBoiBoy and Fang together hand in hand to beat Jo Ejo combat robots. To facilitate the work, BoBoiBoy split into three and use the new combo moves, while also using Dragon Shadow Fang. Finally, they managed to destroy P.E.T.A.I .. So, Ejo Jo had to beat them to wear suits shield alone. At the same time, Adu Du try to repair the robot Mukalakus to help BoBoiBoy beat Ejo Jo for revenge for Probe.