Episode II/III: Thanks to Jango's aforementioned idiocy, Obi-Wan discovers that the records in the Jedi Temple have been tampered with. He heads off to Kamino and discovers a secret clone army, ordered years ago by someone impersonating a dead Jedi. Both of these point to someone with significant power working against the Jedi, likely from within the Republic itself. Yet incredibly, in the years afterwards that the Clone Wars raged, nobody in the Republic ever thought to maybe investigate this suspiciously convenient army or look into how they're being made and trained; if they did, they might have noticed that all of them have an anti-Jedi kill-order hard-coded into them from birth.
Ironically, it was a handful of the clones themselves that wound up investigating that. It did not go well for them.
Too many favorite moments in Star Wars for me to pick a specific one. Though Maul vs. Sidious is probably my favorite saber fight.