BoBoiBoy has just Tok Aba's house to help him around his cocoa stall. There he met and befriended Gopal, Yaya and Ying. Meanwhile an alien known as Adu Du has found out that Tok Aba's cocoa is the strongest energy source. He sent his robot Probe to steal some cocoa sample but was busted by BoBoiBoy who followed probe into the spaceship. BoBoiBoy manage to get the cocoa back but little that he knew, something followed him home.

BoBoiBoy started training to control his new powers. BoBoiBoy tried to explain the powers to his friends when Adu Du attacked them. During the fight, BoBoiBoy was caught. Ochobot gave powers to Ying, Yaya and Gopal to defeat Adu Du and Probe. It was discovered that BoBoiBoy was able to separate into three. Later, Adu Du sent robots to infiltrate and steal cocoa from Tok Aba's shop. Tok Aba was shocked to see BoBoiBoy and his friends possessed super powers.

Gopal got help from BoBoiBoy to find out his power. Meanwhile, Adu Du sent Multi-Monster -a monster that could split into multiple pieces if defeated once -to eat BoBoiBoy.Adu Du's plan failed when Multi-Monster split into dozens of small creatures. Thus, Adu Du decided to kidnap BoBoiBoy's friends. Probe captured Ying after he tricked her with sleeping gas.

Yaya was caught right after Ying. When Gopal was captured next, he finally found out that he could turn any object into food. The four friends then raced for the exit.

When Tok Aba told BoBoiBoy to deliver the cans of cocoa to his customers, he separated into three to facilitate his work. He used his power too long and as a result, he suffered from a temporary memory loss. Meanwhile, Adu Du and Probe infiltrated the cocoa shop to steal Tok Aba's secret recipe book by disguising themselves but were recognized by Yaya and Ying. Probe upgraded in his super form and attacked them all. BoBoiBoy divided himself again even though Ochobot forbade him to do so. BoBoiBoy's memory then got worse. When Adu Du and Probe managed to escape from the trap made by BoBoiBoy Earth, he stole the book and kidnapped BoBoiBoy Lightning.

To obtain the secret recipe, Adu Du, Probe and Computer tortured BoBoiBoy Lightning by exploding balloons until he upgraded to BoBoiBoy Thunderstorm. Adu Du and Probe took advantage of his memory problems. After that, Adu Du and BoBoiBoy Thunderstorm became friends. When BoBoiBoy returned to Tok Aba's house, everyone was irritated as he claims himself "Ada Da", a name given to him by Adu Du. Luckily, when Probe said BoBoiBoy's catchphrase "Awesome!", his memory began to return.

Adu Du decided to torture BoBoiBoy again by trapping him and Gopal into a video game starring Gopal's favorite superhero Papa Zola. Probe was in the game too to torture the heroes. Ochobot and Tok Aba had no choice but to play the game. Yaya anad Ying took their turns too. In the end, they won the game thus releasing BoBoiBoy, Gopal and even Papa Zola out of the television.

Papa Zola, who emerged from the game, appointed his biggest fan Gopal as his student. Later, Papa Zola fainted when Yaya offered him her biscuit. The Sleep Monster, Probe and Adu Du paid a visit to Tok Aba's house. The Sleep Monster made Tok Aba and Ochobot fell asleep. Then, both Ying and Yaya were trapped in the monster's dream bubbles. Papa Zola, Gopal and BoBoiBoy decided to enter the dream bubbles to save the others. Nevertheless, Papa Zola and the Sleep Monster played a game of checkers while the others were stuck as the pieces.

In order to save the gang, they must win a game of checkers against Sleeping Monster, but Papa Zola himself did not know how to play. He lost in the first round. Fortunately, Tok Aba woke up to replace Papa Zola and fought the monster with his skills. Tok Aba and the Sleep Monster had a competitive game of checkers until the third round. The Sleep Monster had to cheat in order to win the final round. However, Tok Aba won the game. The monster couldn't accept his loss so he put Tok Aba, Ochobot, Yaya and Ying to sleep again. Papa Zola passed out after his foot got hurt by a large broken piece of the chessboard. However, BoBoiBoy managed to defeat the monster and everyone was safe.

Adu Du ordered Probe to steal all of BoBoiBoy's fan letters and asked him to answer it rudely but instead, he and Computer answered it honestly (expect rewinds of some clips of some episodes and some rather funny exchanges between Probe and Computer). Adu Du, who returned to the spaceship from shopping for new clothes, scolded Probe for not answering the fan letters rudely.

Gopal, Ying and BoBoiBoy were shocked that it was the World Biscuit Day, because Yaya would ask them to help her make biscuits. As Gopal and Ying ran away, BoBoiBoy Wind had to help Yaya while the other fractions stayed at the cocoa shop. Adu Du tricked BoBoiBoy by making him use fake goat milk that contains "X Solution" -a substance that can make human feelings unstable -as an ingredient for Yaya's biscuits. BoBoiBoy Wind ate one of the contaminated biscuits and distributed all the biscuits without realizing the impact that would be encountered. Yaya's biscuits had caused almost all the people in the town to be insane. The situation became worse as BoBoiBoy Wind ate the biscuits too much, which made him feel an infinite joy. As a result he was transformed to the new power of "BoBoiBoy Cyclone".

BoBoiBoy Cyclone forced Adu Du to eat Yaya's biscuits. Adu Du and Super Probe thought that moment was a good chance to attack him but he was defeated. Unfortunately, BoBoiBoy Cyclone shifted attacks to BoBoiBoy Lightning. Fortunately Ochobot managed to calm BoBoiBoy Cyclone by forcing him to watch a telenovela. Meanwhile, furious about his defeat, Adu Du called Bago Go, a weapon vendor to buy illegal weapons. Adu Du fainted as the price offered by Bago Go was extremely expensive. Probe made the situation worse when he sold Adu Du's spaceship for an Electric spatula. Interestingly, the purchase came with a free mysterious robot package called Mukalakus. Meanwhile, Gopal, Ying and Yaya became devastated because BoBoiBoy would leave Rintis Island in 3 days.

BoBoiBoy was persuaded by his friends to stay in Rintis Island, but then disturbed by the Adu Du's Destruction Robot, Mukalakus, with energy generated by Tok Aba's Cocoa surplus and later, Ochobot (he was caught by Probe). Adu Du easily defeated BoBoiBoy's friends. The fight was so intense that BoBoiBoy Earth forced himself to transform into BoBoiBoy Earthquake. Together, the 3 BoBoiBoy destroyed Mukalakus. Finally, Ochobot was successfully rescued.

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.