Prototype: Evolution is a sequel to Prototype 2 and the second anime to be presented in the same universe. It centers around a Japanese high school named Shi Seikatsu.
The main protagonist of the anime and the third blackligh being. Orginally a weak willed Highschool student, Shi was always cowardly, over apologetic, insecure and nervous. One night, he investigated a facility owned by Gentek and got exposed to the Blacklight virus. Realizing his new power, Shi was having the time of his life. Unfortunately Shi became tired of being treated weak and taken advantage of, that he became a shadow of his former self. As his time with the power progressed, Shi became a rude, violent, arrogant, aggressive, fearless, sadistic and vengeful sociopath, nearly devoided of compassion. He soom made his hair spikey and took on a bad boy image to resemble the infamous Alex Mercer. He also held little respect for his past life considering his old self a to be a "weak pussy". His powers are mixed between Mercer's metallic coloration and James Heller's fluid organic abilities. By season 2, Shi has become alot more malevolent and villainous that he became alot like Alex Mercer in Prototype 2. He later became the main antagonist in season 2.
A shy and beautiful classmate of Shi. Unlike most of the class, Yui was the only one who truly cared for Shi. Yui had a crush on him. She often thought Shi was funny and easy to around with. She was the only one who knew about Shi's newfound superhuman abilities. As time progressed, she soon started to fear that Shi's powers corrupted him and was disgusted with his new ruthless attitude.
Shi's troublemaking friend and a ladies man. Asahi often gives him advice, which ends up getting Shi in trouble for his own amusement. When Shi spiked his hair, Ashai was later mistreated by him, as revenge for being such a bad friend.
Aya is an arrogant straight a student who looks down at Shi. When Shi spiked his hair, she was often dogged and called a "bitch" by him. Shi also developed a strong intolerance for her physical and verbal abuse that he would do the same to her.
The leader of the Blackwatch forces in Japan. Ruthless and determined, Riddic believes Shi to be a threat to mankind just like Alex Mercer.
Returning as the main antagonist of the series. It is also revealed that Nox was Elizabeth Greene's son, Pariah.
Returning as Shi's mentor. He also appeared as the main protagonist in Season 2.