After the creation and failure of the Paradise Matrix, The Architect created the Nightmare Matrix and based the design of that Matrix beta off of human beings' perception and violence towards one another, the reason for why the first Matrix was a failure. Within the Nightmare Matrix, The Architect created supernatural monsters to fit the environment and situations for bluepills.
Cain, along with fellow werewolf program Abel and phantom programs of The Twins, were created and situated within the nightmare matrix. After realizing that the Nightmare Matrix was another failed Matrix beta, The Architect rebooted the system and deleted all existing programs created for the Matrix.
However, before Cain, Abel, and other programs were deleted, The Merovingian protected all of the programs he thought will be of good use for him and saved them from deletion.
Upon rescuing them, the surviving programs started to work for The Merovingian in helping him and his wife Persephone with whatever deeds they requested.
Serving The Merovingian
But Abel foiled the plan by telling The Merovingian about the betrayal. Eventually, the key was destroyed by The Merovingian, forcing The Keymaker to create another one.
Persephone then threatened to kill Cain too if he did not run and tell her husband what she had done. He quickly left to tell his boss about what his wife was doing with the Resistance.
Battle with The One
After retrieving The Keymaker, Neo and the others attempted to leave the Chateau but was interrupted by The Merovingian and his henchmen. After Persephone left her husband to deal with the Resistance, The Merovingian ordered The Twins to go after The Keymaker. The Keymaker fled the scene and Neo ordered Morpheus and Trinity to go after him while he deals with The Merovingian and his men.
After Trinity and Morpheus left, The Merovingian ordered his men to fire their guns at Neo but being gifted with the Prime Program, Neo stopped all of the incoming bullets from impacting him and a battle within the Chateau took place between Neo and The Merovingian's henchmen.
As the battle began, Cain, along with another exiled vampire program, attacked Neo with jumping spinning kicks. Neo dodged all of Cain's attacks and after blocking an exile's triple jumping front snap kicks, Neo quickly approached Cain and performed a front snap kick to Cain's chest. The impact caused Cain to fly across the room and crash through the mounted statue near the foot of the staircase and hit his back on the wall.
After the impact on the wall, Cain landed chest-first on a one of the broken statue pieces and impacted him on the heart, killing him while the fight was still in progress.
Behind the Scenes
In the theatrical releases he is portrayed by actor, director, stunt coordinator David No. Cain, the exile program, who was aptly named for the biblical brothers except in this case, Abel was killed by Persephone not by Cain, and Cain was killed in the battle in the foyer of The Merovingian's Chateau.