Best boss fights were
Omega Zero (Mega Man Zero 3)
This fight was...well, there are no words to explain, but this was really deep, and was the second time Zero had to confront himself, only this time, he was fighting his real body usin' the duplicate one created for him. The end of the battle also marked the true end of Mega Man X's life
Copy X (Mega Man Zero)
A sinister take on the Vs. X battle from Mega Man X5. You have to keep in mind that you are fighting a doppelganger who fancies himself as a hero, due to his role as leader and supposedly an angel. In an unexpected twist, Copy X is the only Mega Man incarnation to possess a final form
Sonic/Shadow2 (Sonic Adventure 2)
To date, this is still the most fast paced battle in the series. You are fighting against a figure who possesses the same powers as you and runs as fast you do. The music and atmosphere further intensifies the feeling of it all
Weil/Ragnarok (Mega Man Zero 4)
The final battle for both the series and Zero himself. Described as Zero's Finest Hour, absolutely everything was at stake here. Zero had to race against the clock to defeat the now completely insane and suicidal Weil and the music that played in the background signified that THIS was the battle to end all battles. This boss battle marked the first official conclusion of a series, but at the cost of Zero himself. Ironically, the same machine that was meant to destroy the world ended up saving it.
Dark Link (Link's Awakening, Ocarina of Time)
Yush, another doppelganger. Dark Link himself was an entity completely shrouded in mystery. The only thing known about Dark Link was that he was everything that his counterpart wasn't. Basically, this battle was a true testament of conquering yourself, meaning you had to exploit your very own weaknesses to defeat this shadow-bound creature who was capable of doing everything you knew and then some.
Ganon (Ocarina of Time)
Arguably the very first epic final boss battle. The atmosphere of the battle was intensifying. You were now fighting the classic form of the sorcerer steeped in darkness and corrupted by the misuse of the Triforce of Power. Before you even got to cross swords with him, Ganon would throw a wild fit, knocking the Master Sword out of your hand. Worst off, you could not just simply walk away from this battle as the arena was surrounded by a circle of fire, barring your path from the Blade of Evil's Bane. He had to be weakened enough for you to retrieve it back. After that, he could only be defeated by that sword specifically.
So yeah D:
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