Season 2
The second season consists of 13 episodes, it was aired on Sunday, 27 May 2012 at 7:00 pm on TV3. In this season, BoBoiBoy begins a new chapter of his life as he moves to Pulau Rintis to reunite with Tok Aba Bin Abah Kau, Gopal, Ying and Yaya. The story in this season mainly centres on BoBoiBoy and his friends' life at Pulau Rintis Primary School. BoBoiBoy also encounters a new challenger, Fang at his new school. Fang or Mystery Boy was first introduced in Season 1 on Extended Finale episode. In Season 2 finale BoBoiBoy's friends along with Fang fight a super-powerful alien named Ejo Jo who takes all the power watches except for Fang and Boboiboy, and to defeat him, Fang uses his full power.
Episodes
1 Welcome Back, BoBoiBoy! May 27, 2012 
2 The Haunted House Jun 3, 2012 
3 Physical Education Jun 10, 2012 
4 Football Fight! Jun 24, 2012 
5 Late for School Aug 26, 2012 
6 Giant Mini World Sep 9, 2012 
7 Emotive Chemical Y Dec 9, 2012 
8 Fang and Ochobot's Secret Dec 16, 2012 
9 Mornings with Mr. Probe and Adu Du Dec 23, 2012 
10 First Contact Dec 30, 2012 
11 Pop Quiz Season Mar 10, 2013 
12 Ejo Jo Attacks Mar 17, 2013 
13 Goodbye, Probe Mar 24, 2013