Believe it or not I am a big fan of this game's Single Player Adventure. Call me crazy, but I LOVE reading the Logbooks in every Metroid Prime game, they have such a beautiful and rich story that I enjoy a lot. However, throught out the game, there were some completely unexplained things that made no sense whatsoever, I will try to mention some, and explain some if possible.
Sylux's Crashing Ship on Alinos In a certain part of the game, when you look for the second Octolith of Alinos, in a scene you see Sylux's ship full of smoke in it's back. It has a crashing fashion. I expected I would meet Sylux and battle him again or some twist in the Story Mode, but nothing actually happened? Where was Sylux? If his ship actually fell on the Crashing Site were the third key to open the Boss Portal was, how could he fly to Oubliette? Did he fix it? Why there is no sight of his ship there? Such enigma.
The amazing tornado from Celestial Archives This also occurs when you search for the second Octlith. When you enter the famous Transfer Lock (my favorite stage, looks so awesome) you see a whole tornado, or is it a galaxy, above you. It seems to be composed of dust, it's rare to see a Tornado where there is no wind in the far-off of space.
Celetial Archives' Destroyed Vista and New Found Place Those rooms around here represent the huge damage done by Gorea when he started attacking.
Strange fluid and monster on the Battlehammer room In the room where you find the Battlehammer, an odd, organic-like substance is around the room. A strange monster who is never mentioned is also present in the Morph ball way, its mouth is full of that substance.
How did the Alimbics obtain the Hunter's power beams? This is a big mystery, how did the Alimbics possess weapons of far, unknown to them nations? They possesed the Battlehammer, Imperialist, and even the Missiles that were made by the Chozo. Odd, right?
The generator from Vesper Defense In the final edge of this ship, the huge Generator that is slowly blowing up and you have to shut it down, in MUltiplayer it functions as some sort of elevator. However, do it in Single Player mOde, and it will instantly kill you, instead of levitating you!
I will add more soon, I still will add around 3 more weird stuf!!! --- "Behold my powers! I am the most powerful Pokemon in the world!" -Mewtwo 3DS FC: 4339-2716-5379