The Animatrix EP9 - Matriculated

The film deals with a group of above-ground human rebels who lure hostile machines to their laboratory to capture them and insert them into a "matrix" of their own design. Within this matrix, the humans attempt to teach the captured machines some of the positive traits of humanity, primarily compassion and empathy. The rebels' hope is that, once converted of its own volition (a key point discussed in the film), an "enlightened" machine will assist Zion in its struggle against the machine-controlled totalitarianism which currently dominates the Earth.

The film starts with a human woman Alexa (Melinda Clarke) looking out over the sea, watching for incoming machines, where she sees two "runners," one of the most intelligent robots, approaching. She leads them into the laboratory, where one runner gets killed by a reprogramed robot, but the second runner kills the robot before Alexa electrocutes it. The rebels insert the runner into their matrix. The robot experiences moments of mystery, horror, wonder and excitement, leading it to believe it may have an emotional bond with Alexa.

However, the laboratory is attacked by Sentinel reinforcements. The rebels unplug themselves to defend their headquarters, along with the help of other captured machines (indicated by the machine's mechanical eyes changing from red to green). Alexa unplugs the runner that has now turned good, where it saves her from a machine. The rebels and the attacking machines are all killed or destroyed, except for the runner. The robot plugs the dying Alexa and itself into the rebels' matrix. When Alexa realizes that she is trapped inside of the matrix with the runner, she is horrified and her avatar screams and dissolves as the runner exits from the rebels' matrix to see a dead Alexa in front of him in the real world.

The film ends with the "converted" runner standing outside, looking out over the sea, in a replica of the opening shot with Alexa.