Not sure if it’s exactly a plot twist, but the fact that the whole Matoran Universe (sans Mata Nui island) was actually inside the Mata Nui robot was a bit confusing to me at first.
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That still confuses me to this day for multiple reasons.
I was mainly confused by the fact that the MU consists of islands. That brings up two main questions. One is that when the Mata Nui robot became functional again in 2008, shouldn’t gravity have tilted each landmass causing cataclysm all around? The other is if the islands were indeed grounded within the robot, that would mean they should have developed after Mata Nui crashed and became dormant, thus going back to the first question of how the MU works in terms of it being inside the robot.
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That post sums up my confusion.
Bionicle- where laws of physics don’t need apply.
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The biggest plot twist for me was when I was a kid and I bought a blue toy because blue was my favorite and then I found out it was a girl 
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There is an artificial gravity inside the robot generated to keep everything oriented so that towards Mata Nui’s back is down and towards his chest is up at all times, no matter which way the robot is actually angled. And the islands inside the Mata Nui robot were all created when the robot was built, as habitation for the Matoran and other species.
I personally don’t know my favorite plot twist, maybe finding out the MU was a robot.
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Oh wow, exact same situation for me. And I even consider water my main (although not necessarily my fav) element. :-/
I figured that was the case, but then how would one travel throughout the system?
Tubes. or Red Star. Don’t exactly know the question.
My favourite has to be when Matoro made the ultimate sacrifice and died to revive Mata Nui, and then in Metru Nui, the stars form along to create the Kraahkan, the mask of Makuta.
I can just imagine the wind whistling like normal, and then it becomes a sinister laugh.
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That it’s not ending.
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I did the same thing, bought it was cool and finding out it was a girl years later
Speaking of which, I feel like there should be both genders in a race of matoran. Because unfairness
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The turaga being toa in the past.
The biggest was the red star. From the very first year of Bionicle we knew about it, but I doubt many figured out what it’s actual purpose was until it’s final reveal in 2010. However, this wasn’t really a ‘best’ plot twist. It made many of the characters deaths seem less amazing.
My favorite plot twist? Makuta jumping into Mata Nui’s head not two minutes after he’s been awoken (Seriously, the Toa took 8 years [technically 1 in bionicle time, but still, WE took 8 years] and then Makuta goes and steals Mata Nui’s body!)
I actually suspected the matoran universe was inside some sort of robot for a long period of time. The whole route of travel between the Mata Nui and Metru Nui islands tipped me off. It seemed strange that the Mata Nui island just ‘floated’ above Metru Nui. There had to be some sort of explanation, right?
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Honestly, I was completely okay with the Red Star being what it was. How many character deaths were that interesting? Lhikan and Mavrah. Maybe Zaktan. Most of the Makuta and Matoro have been confirmed to not come back. Most other deaths were back-story deaths. Then there are characters like Ancient who had just gotten interesting when he died.
On topic though, I totally called Velika being an evil space god.
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Has it actually been confirmed that Zaktan died and he’s not just in control of the Golden Skinned Being? because that’s what I got from the inclusion of him in that story.
If somehow all the serials would remain canon in 2015 that would be a great plot twist.