Dirge of Cerberus: Final Fantasy VII
The Protomateria is an extremely rare form of Materia that was found by Lucrecia Crescent. After Professor Hojo's experiments, Vincent Valentine's body was capable of holding the Chaos gene. However, it came at a cost, as he couldn't control himself when he changed into this form. The Protomateria helps Vincent control Chaos and it is inserted into his body.
Vincent is completely unaware that he has an extremely powerful Materia inside his chest, as although Lucrecia performed the operation, she didn't ever tell him what was actually done to him.
Needed To Summon Omega Weapon
After studying Lucrecia Crescent's research, Hojo is able to establish that the Protomateria is necessary to activate Omega Weapon. He then orders the Tsviets to find it, which means they start hunting Vincent.
Even though the Protomateria is ripped from Vincent's chest and then used to summon Omega Weapon, Vincent, with the help of Shelke Rui, manages to have it reinserted into his chest for his confrontation with Omega.
Destroyed By Vincent Valentine
Towards the end of his confrontation with Omega Weapon, Vincent uses the awesome power of the Protomateria to its full effect. He essentially turns it into a huge bomb which then explodes and destroys Omega.
Somehow, Vincent manages to survive the explosion, but it is believed that the Protomateria was obliterated after this act was carried out.