The Hunters go to Gate's laboratory to put to a stop to his plans. Following Gate's defeat, he confesses he has rebuilt Sigma, and was using him as a trump card, but Sigma is a shell of his former self: a partially coherent, half-built body, with his programming still severely damaged. However, Sigma has enough strength to nearly kill Gate, and challenges X and Zero. With his sanity slipping, Sigma is once again defeated and one of three endings will occur, depending on which character defeats Sigma: