In Batman & Mr. Freeze: SubZero, Mr. Freeze's wife Nora is in desperate need of a transplant to save her life. However, her rare blood type makes it difficult to find a suitable donor. Mr. Freeze turns to his old partner, Dr. Gregory Belson, who had developed cryogenic freezing technology and had previously saved Freeze's life, for help. Belson suggests using a transplant from a living donor, so Mr. Freeze targets Barbara Gordon, who has the same blood type as Nora.
Meanwhile, Batman and Robin are on a mission to destroy a giant floating laboratory that has been conducting illegal genetic experiments. During the mission, they receive a distress signal from Barbara, who has been kidnapped by Mr. Freeze. Using their detective skills, they track down Mr. Freeze's hideout and engage in a battle with his henchmen.
Batman and Robin eventually rescue Barbara, but they discover that Mr. Freeze's plan was to transplant Nora's head onto Barbara's body. They rush to the location of Belson's cryogenic lab, where the transplant operation is about to begin. In a final showdown, Batman and Mr. Freeze fight while the lab collapses around them. Batman saves Mr. Freeze, and Nora's head is restored to her specially designed cryogenic suit.
As Mr. Freeze mourns the loss of his wife's body, he finds solace in knowing that she is at least alive. Batman admits that he understands Mr. Freeze's desire to save his wife, but tells him that kidnapping people is not the right way to achieve his goals. The movie ends with Mr. Freeze being taken back to Arkham Asylum and Batman and Robin driving off into the night.