Freeze is introduced in the episode "Heart of Ice", which won an Emmy for Outstanding Writing in an Animated Program. Freeze leads a band of henchmen and makes several raids on the company Gothcorp, stealing the parts for a freezing machine he wishes to build and use in his battle against the company. This leads to his first confrontation with Batman, whom he defeats easily and traps in a block of ice. Later on, before another attack on Gothcorp after the machine is complete, Freeze catches Batman in the security room, watching an archive video revealing Freeze's tragic origin. While working for Gothcorp, Victor Fries had been using illegal funding for an experiment to save his dying wife, Nora, by cryogenically freezing her to preserve her until a cure could be found. At the last moment, however, the ruthless Gothcorp CEO, Ferris Boyle, had broken into the lab with guards and kicked Fries into a batch of chemicals, leaving him to die. Fries survived, but was severely mutated by the substances and transformed into Mr. Freeze. Now, on a vendetta against Boyle, Freeze traps Batman and leaves him in his hideout, confronting Boyle at the Gothcorp Humanitarian Party and freezing him up to the waist. Batman, however, escapes and confronts Freeze at the party, fighting him one-on-one until he breaks Freeze's helmet with a flask of chicken soup. Freeze is defeated, and arrested along with Boyle, as Batman presented evidence of Boyle's crimes to the press. Freeze is then imprisoned in Arkham.
Freeze later appears in "Deep Freeze", where he is sprung out of prison (against his will) and taken to an off-shore city named Oceana by an android owned by theme-park builder Grant Walker, who is fascinated with Freeze and needs his technology to condition his body to become like Freeze's, for his maniacal plan of a Global Deep Freeze to create a new world for his selected residents of Oceana. Freeze, at first, refuses to help Walker, but when Walker shows Freeze his wife, alive but still cryogenically frozen, Freeze accepts. Batman and Robin arrive and tell him that if Freeze helps Walker freeze Gotham, Nora would hate him. Freeze finally sees the truth, and helps Batman and Robin stop Walker at the last minute. Freeze battles Walker, who has been placed in a cryo-suit identical to Freeze's, and wins by pinning Walker to a wall with his gun. Freeze then proceeds to overload Oceana's power-core, blowing the city to smithereens and warning the inhabitants to flee for their lives. Freeze opts to stay behind and die with his wife, and freezes Robin to stop Batman from following him. Freeze, Nora and Walker disappear in the explosion, but the episode's end reveals that they all survive, temporarily trapped in icebergs.
While BTAS style of revising various smaller Batman villains, none were as successful as Mr. Freeze, who had been introduce in the comics as one of the many gimmick oriented enemies of Batman with little depth or detail. The character's was completely altered for the series, with a sympathetic backstory, including his wife Nora, and great moral complexity, with the character's cold, stoic demeanor coupled with a barley restrained vindictive fury, much like Batman himself. Freeze was very popular with fans and the comics soon changed to include the new rendition with a swiftly resurrected Freeze, who was killed by the Joker at the time.