Mewtwo, long before he was born, thrived in a drifting sleep. In his subconscious, he met another creature, a young human girl, who understood from the start that he was alone, just like her. At this stage in life, Mewtwo was basically a helpless child (erm, kitty? ^^
. Ai realized this, so she dedicated the rest of her existence toward educating him with the knowledge she had, with an extreme selfless compassion. It's not surprising that they soon bonded in friendship, and Mewtwo respected her as a mother-figure.
However, Mewtwo clearly knew that Ai wasn't his mother. Never once did he ask her this, nor did he ask her if she was related at all. He clearly knew that she was his best friend ... his only true friend. The bond they shared was innocent and beautiful. It lacked competition, faults, and judgement. Ai accepted Mewtwo for who he was, as did Mewtwo for Ai. They never saw each other for what they were, but for who they were. Of course they interacted with Bulbasaurtwo, Squirtletwo and Charmandertwo, but they pinpointed their attention on the joy they received from each other.
When Ai began to die, her devotion to enveloping Mewtwo in happiness still burned. As he cried, questioning what tears were, Ai assured him that tears are filled with life. She always made sure to answer his questions truthfully, but on the positive pole of it. As she faded, she told him, "Don't cry, Mewtwo. You should be happy! You're alive, and life is wonderful..."
Mewtwo continued to cry out for her, into adolescence, anxiously wanting hear her genile voice again. While this went on, he was sedated by the scientists, because his brainwaves became severely unstable after Ai had died. He was sedated so he'd forget her. However, that happened when he was still a child. And he did remember her into adolescence. In my opinion, I believe his care for her was so powerful that it was able to break past the sedatives. And eventually, due to being so traumatized, his subconscious blacked out his memories of her (For some people, when they are highly traumatized, the subconscious has been known to do this, according to studies). It would only make sense that he caused himself to blur his memories of her so he could thrive on with his life, yet deep in his soul carry the emotions he has for her.
Ai dedicated herself to the welfare of Mewtwo's happiness, as Mewtwo gave himself to having trust and faith in her.