I heard this on RedLetterMedia's commentary track and was wondering if this plot-hole can be resolved.
Here are some more stretches in logic and general assumptions by even more characters. When you stop and think about things, nothing makes sense even more, if that's even possible.
So the very first and most recent appearance of this mystery Sith character was on Tatooine, when he attacked Qui-Gon.
Now remember, Qui-Gon is not at all aware about Lord Sidious. The audience knows, but he doesn't know. In fact when he got on that ship in the beginning he didn't sense anything odd. As far as he's concerned this is all a tax dispute thing that got out of control. So then this guy in black robes leaps out of the air and attacks Qui-Gon, and he makes the assumption that this guy was after the Queen.
Why did you think that?
If he was after the Queen all he really had to do was stab the ship with his lightsaber and run away. That would've messed it up a little, stab some critical engine part or something.
From Qui-Gon's perspective, why would this Sith Lord care about a blockade and a tax dispute on some faraway planet? That's quite the leap of logic.
Also the Sith are like the yang to the yin, as far as the Jedis go? They're the opposite of them?
Let's not forget that Qui-Gon just discovered this little boy who is with him right now, who has more midi-chlorians than Yoda, and he's also supposed to be the Chosen One, and Qui-Gon doesn't even mention the idea that maybe this guy was trying to kill him? I mean, he does try to run him over with his speeder. But no, he's probably going after Queen Amidala because almost no evidence points to that.
Then based only on the hypothesis that this guy may have been after the Queen, the Jedi Council thinks that Qui-Gon and Obi-Wan should go back to Naboo to discover the mystery of their attacker. Uhm, how do any of you know that Darth Maul is going to be on Naboo? Did you all read the script?
The only explanation they have is that a weird guy trained in the Jedi arts attacked them on Tatooine. This guy could have just been living on Tatooine and wanted to steal Qui-Gon's gin.
- Source (From 1:16:57 to 1:20:00)