No one knows what to make of the mysterious new NetNavi Bass, but everyone is intrigued when it seems that he alone can resist the CyberBeast that's slowly destroying the entire Cyber Network! What will he do with that kind of power? What does he want? And whose side is he on: MegaMan's? Grave's? Taking no chances, Kid Grave sends FreezeMan to delete Bass. Then Bass makes off with an unconscious MegaMan, launching Lan and his friends on a desperate search to find him. And worst of all: Mr. Wily has returned.

Years in the past, Cam arrives at the Wind Ninja Academy. Claiming to be a new student, he enters to look for the needed power source before he has to return to the present. He encounters younger versions of his parents (Kanoi and Miko, the first female student in the Wind Ninja Academy) and a previously unheard of uncle (Kiya). Cam discovers that Miko owns the powerful Samurai Amulet. While getting to know her, he doesn't openly tell her who he is, but mentions if his mother ever saw what he was doing, she would be disappointed in him. Miko assures Cam that she would be proud of the person he was becoming. Before he can do anything about it, he is framed for its theft. However, before the Sensei could give judgement, Kanoi interrupted, revealing Kiya not only to be the true thief, but practicing the forbidden dark ninja arts. Kiya then attacked the Academy, but Miko is able to kick it away to Cam who challenges him for it. He and Kiya fight in the forcefield he created. After a long battle, Cam defeats him wand the amulet's powers reveal his future as Lothor before breaking the barrier. Kiya is held down and restrained by two of the students. Disappointed in Kiya for stealing the amulet, framing Cam for it, and using dark ninja powers, the Sensei stripped Kiya from his ninja rank, expelled him from the academy. Before being banished off he warns Kanoi he will be back for revenge for his betrayal and denounces his name to become Lothor. Cam ties to stop it, but the sensei holds him back and places Kiya in an orb of light to be imprisoned in for a long time. He banishes Kiya into space, where he believed that his dark powers could do no harm. Cam warns the Sensei that they need to destroy Kiya now before it's too late. The sensei reminds him that they can only judge by the present actions, not the future that is unseen. Cam mentions the Sensei should trust him because he knows what he's talking about. He points out they need to destroy Kiya now before it's too late because he has seen into the future and it's not good. But then the scroll lights up and he's out of time. Cam wanted more time to get to know Kanoi and Miko. She bids Cam farewell and he goes back to the present. On top of that, Cam returns to the present and saves the powerless Rangers from Madtropolis.