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Disclaimer
This is a personal list using games I've personally beaten. You have a difference in opinion please post on the bottom. Since I've never personally beaten a Metal Gear Solid game, Psycho Mantis will not be on this list. Also I'm using boss fights that are either puzzles or using psychic energy, with a few final bosses that I find are great at strategy and only force of will defeated them in their game. So to make this list, it has to be from a game I beat, and has to either have psychic energy, or be incredibly intelligent of a foe. There is one fight in here that is a puzzle boss (a set of three) but I find they sense more then we do using psychic energy so I included them as well. Thank you.
WARNING possible spoilers WARNING
Pix is not the most memorable boss. Heck if it wasn’t for the picture even people who played this game would be asking who. Is this a boss a puzzle boss? No. Psychic energy? That is the one. I didn’t really find any information on what these things are but I guessed psychic matter. They do have color coded weaknesses as well so that is kind of like a puzzle. There are of course better Kirby bosses, but none exactly like this.
For some weird reason this character is far more popular then I imagined. Anyway, Doopliss fits the mind game category even though he clearly uses darkness energy. Doopliss is a puzzle in a way, as you actually have to go find out his name, and you aren’t allowed to guess it either. See he makes Mario into a shadow and takes Mario’s form, forcing Mario to team up with Vivian and continue onward until Doopliss is defeated. Pretty crazy.
A powerful being made of… well it never says, the psychic energy of subspace I assume. He is a stategist using Game and Watch as well as Master hand to take over an entire world. He is a strategist and to fight him is a strength of determination, and him being possibly made of psychic energy certainly helps. He is a powerful fight, and despite a stupid powerful move, Tabuu is a fun and difficult fight.
Well this fight kind of almost made up for the horrid boss fight with Silver in Sonic 06. I still have that game and may do a review of it eventually. For now, let’s say the Sonic Generations fight with Silver is pretty good. It is a little confusing at first, but a decent rival battle, and he uses psychic energy as well which helps. Too bad Silver didn’t play like this in 2006.
The psychic type gym leader certainly bent your mind the first time you go after her as there isn't really anything great against psychic type pokemon back in the day. Kids today are spoiled with Dark type pokemon. Anyway, Sabrina was a powerful foe with powerful psychic pokemon making her one of the toughest Kanto gym leaders despite not being the final gym leader. There isn't (or wasn't) too much background to her though so defeating her was a test of power and nothing more.
Intelligent and boggles the mind of Altair with an Apple of Eden, Altair ends up in a fight with all the templars he has killed during the game. Al Mualim is intelligent and power hungry out for the same thing the templars are, but not loyal to them. Unfortunately he created the assassins the templars greatest enemy as well. This final boss fight is probably one of the better final bosses of Assassin's Creed history, and boy is it good.
Despite not leaving the temple, these sisters can sense things happening in the past, present, and future of the world. Not only that but they are puzzle bosses and fighting the sisters kind of warped the mind. This was one of the better parts of God of War II and well worth it to finally destroy the bonds of fate so Kratos could kill the gods in the third game. A great boss fight and a mind scratcher to boot.
When it comes to intelligence in the Marvel world, not many can stand against Reed Richards and Victor Doom. In Marvel Ultimate Alliance, you and a large team of super heroes are racing to stop Doom's master plan as he tries to capture the powers of Odin himself and uses Loki, Ultron, Baron Mordo, and Enchantress to do so. The final fight with Doom, who is basically Doom plus Odin, is awesome, and since Doom uses his new mind bending reality altering powers to make evil versions of super heroes, it doesn't get much better then that.
And DC comics wins. No offence, I love Marvel comics more, but I cannot deny the Riddler his glory. If Scarecrow from the first game can be a boss fight, then Riddler can be in the second game. He traps innocent people in deadly traps for Batman to solve, forcing you, the player, to get creative and solve the puzzles Riddler plans out for you. It is a battle of minds at its finest. If you beat his mind games enough times, then you finally get to take down and beat the Riddler once and for all, making him far better then Dr. Doom. Only one crazy mind bending foe can beat that...
While the game may not have been the strongest in the series, Twilight Princess had some of the best boss battles of all time. Stallord took the Undead list by storm, and now Zant is bringing up the madness and mind hurting boss fight he had in Twilight Princess. It is mostly a memory game as he changes his powers and abilities. All this time Zant was acting collected and cool, with his calm demeanor, but it turns out he is a spoiled brat, and like most arrogant killers he has a break down when finally caught and confronted. The boss fight that follows is amazing as you fight him like other bosses, only to end in a crazy teleporting sword fight outside of Hyrule Castle. Your brain may hurt after the battle, but it is the best boss battle with mind bending elements there is.