Sasha was never thought to be Team Aqua's leader. In fact, she was not always Team Aqua's Leader. She used to be a normal trainer, trained by Professor Rowan. That is why the professor never knew that Sasha was in Team Aqua. Sasha became so powerful that she decided to join up with Team Aqua to become even more powerful. Since she was so strong and defeated Team Aqua's old leader, Peridot, she was able to move up and become the leader of Team Aqua. One day she met a powerful trainer named Red/Leaf who she followed around, pretending to befriend to get information to take back to Team Aqua. In other words, she was a spy.
Spoiler warning: Spoilers end here.
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