Kirito's Yellow Eyes

Throughout Kirito's various VR experiences, one mystery continues to pop up: why do Kirito's eyes sometimes turn yellow in the heat of battle?

Kirito only tends to bring out his full potential and strength when it really counts. Just as Asuna says, he does this when the virtual world becomes the real world. When the lines between both worlds blur, it is no longer a game for him. In Sword Art Online, death in the game means death in the real world. Kirito gives it everything he has when he fights, especially when protecting those dear to him. 

Kirito earns the dual wielding skill for his superior speed and abilities, and Heathcliff (aka Akihiko Kayaba) has to "cheat" the system to keep from losing their duel. In their final fight, Kirito has the chance to clear the game if he wins. He cannot break through Heathcliff's shield, and his Dark Repulser blade ends up breaking. When he is about to be slashed down, Asuna powers through her paralysis and takes the hit. This causes her to appear to die, which brings down Kirito as he is filled with sorrow. He takes a direct hit, and his HP drops to 0. However, he decides the fight is not over, his eyes turn yellow, and he stabs his blade through Heathcliff to take his life as well. In the end, Kirito and Asuna end up living and watch SAO crumble alongside Kayaba.

When Kirito has to battle against Sugo to protect Asuna, Kayaba's consciousness appears to him. He claims Kirito has the will to overcome the system he once defied (and ALfheim Online was created from Sword Art Online, the system Kayaba speaks of). Kirito is able to use Heathcliff's account to defeat Sugo, and once again he overcomes the system of the game. Kayaba claims this power comes from within himself, not from the admin privileges he used. Kirito is then given the Seed to give birth to a new generation of VR.

In his fated fight with Death Gun, Kirito once again has his eyes turned yellow as he defies death and claims victory. Even in Sword Art Online The Movie - Ordinal Scale, Kirito's eyes turn yellow as he defeats all of the augmented enemies with just one fell blow. When he faces the Pontifex at the end of Sword Art Online: Alicization, Kirito decides to endure, even after losing his right arm. His eyes turn yellow, and he wins the battle. I believe the same goes for his moment of awakening in Sword Art Online: Alicization - War of Underworld, when he fights Gabriel (although I have not watched the anime that far quite yet).

When Kirito's eyes turn yellow, he is defying the system of the virtual world. His will is stronger than the system itself. In the Underworld, this "ability" of his makes more sense due to the link between mindset and strength. In the other virtual worlds, however, Kirito has to overcome the mechanics of the game and the limitations posed. When he must protect those dear to him, Kirito will bring out his full willpower and give his fight everything his soul has to offer, even if it means overpowering the game itself.