9. The Matrix Reloaded
The Twist We Got
In fairness, The Matrix Reloaded actually delivers two climactic plot twists for the price of one.
Firstly, that Neo (Keanu Reeves) has found a way to use his superhuman powers outside of the Matrix, harnessing them to disable a fleet of incoming Sentinels, and secondly, Agent Smith (Hugo Weaving) has managed to reach Zion by possessing Resistance member Bane (Ian Bliss).
The Twist We Wanted
While the precise mechanics behind Neo's ability to manifest powers outside of the Matrix were never explicitly explained in Reloaded or any other Matrix sequel, many fans took it as "evidence" of an altogether nuttier twist, that Zion was in fact another level of the Matrix.
After all, what better way to truly pacify humanity than giving them the illusion of escape and salvation?
It would've totally rewritten the rules of the franchise in a fascinating way, even if it admittedly may have opened a huge can of worms where plot holes are concerned, and certainly wouldn't have gone down well with all fans.