Detective Ross Sylibus recovers from the battle with the D'AnClaude battledroid thanks to robotic prosthetics, but his superiors reject his report about the incident because it contradicts their official stance that D'AnClaude is confined in the Shinora Hospital. His identity as a human and police officer begin crumbling. Meanwhile Armitage and her "brother" Julian, the last of the remaining "Thirds" (formerly referred to as "Threes"), retreat into hiding. Armitage faces the revelation that her design allows her to reproduce and that her creator made her "emotionally perfect" - her offspring would be a human child. She cannot understand why, as Julian puts it, they "created a robot who could kick ass and raise kids." She and Julian break into a mainframe computer and learn that, shockingly, one of their creators was Dr. Rene D'AnClaude, which exacerbates her identity crisis. But before they learn more, the presence of D'AnClaude in cyberspace possesses Julian, causing the penultimate "Third" to melt down.

Learning that the "puppet" robots being used as suicide bombers around the city have the same boards as the "Thirds," Sylibus abandons his badge to shake down the vice-president of the robotics company for answers. Having become a vigilante, he rejoins Armitage and together they enter literal cyberspace, plugging into a computer to search for the "backup" of himself that Julian had stored online. Julian can give them only one piece of helpful information: The real Dr. D'AnClaude is indeed in Shinora Hospital, guarded by the army itself, which would be a more serious problem if not for the final secret revealed in "Heart Core" - Armitage is not a Third-type robot like Julian. She has a Third-type board and chip, but is built as an assassinroid- a type of fighting machine designed by none other than Dr. Rene D'AnClaude whose hospital fortress she and Sylibus now assault.

"Heart Core" is the subtlest and most character driven episode of the series. Sylibus and Armitage have now lost everything except each other. No longer police officers, their professional interest in D'Anclaude's genocidal campaign ends. The robot made too human and the man who has become part robot fight for their lives in a quest to discover who and what they are, and why they have been lied to.

Ochi and Konaka focus more on Sylibus' and Armitage's interior lives and growing emotional relationship than ever before. Reflecting aloud about becoming a robot forces Sylibus to be more demonstrative than is natural for his character. His growing empathy for Armitage also makes him more human than he has ever seemed. He develops a proud, fatalistic tone as he turns his back on everything in his life except the purpose he now shares with Armitage. She also matures from the oft childish character in "Electro Blood." Moments of self-doubt replace her manic tantrums, and more specific emotional dilemmas render her sympathetic.

"Heart Core" avoids falling into the pitfall of wallowing in melodrama by having a thinly distributed soundtrack and relatively spare dialogue, allowing the emotional development to unfurl. Also, director Takuya Sato uses extensive backlighting and muted, low-contrast color schemes within scenes to deflect attention from the amount of emotions that comprise this episode's story. This understated directorial approach demonstrates Sato's skillful and effective storytelling.

Dark irony crops up often in "Heart Core:" Sylibus emoting for the first time now that he has robotic parts; Julian calling Armitage "emotionally perfect," when she is most tortured and confused; Armitage deciding that her life is worth less because she isn't a "real" third-type robot. Occasional comic relief interrupts the somber tone of the episode - a wicked satire of TV newscasters' banter, easily the funniest bit yet in the series. Pointed, but never intrusive, the irony adds complex layers to the series.