The Legacy of Torchwood One! was the first story printed in Torchwood The Official Magazine.
Ianto is walking the streets of Cardiff in the early evening, when Rupert Howarth, his old mentor from Torchwood One, whom he believed to be dead, confronts him. Ianto takes him back to the Hub, where he is questioned by Jack.
Rupert was the head of Torchwood One's Bio-Medical Research Division. He was on the verge of a massive breakthrough in Immunity-Boosting Drugs which would have ended all viral diseases. However, pharmaceutical companies found out and at first tried to bribe, then kill him so they could retain their control over third world natural resources. He faked his own death by burning down his lab and went into hiding.
At the end of Rupert's story, Tosh picks up a police report about something running from a burning warehouse, leaving behind a neat pile of dead bodies. Jack, Gwen and Owen go to investigate the warehouse. Inside: the bodies of homeless people. Gwen believes that the fire and the fact Rupert had been sleeping rough was too much of a coincidence for the warehouse not to be a targeted attack.
As they leave, Jack, Gwen and Owen are attacked by a creature. It looks different to each of them. The creature says that it wants to see Rupert, or those Jack loves will die.
Back at the Hub, Jack confronts Rupert over the creature. Rupert says it's called a Chimera. At Torchwood One they had acquired some alien tissue samples that provoked a primal fear response. They planned to create a hybrid DNA strand to be used by special forces against terrorists. They had tested the DNA on the homeless and drug addicts. All of them had died but one. It became uncontrollable and fought back against its creator, which was the true reason Rupert faked his own death.
Whilst Rupert tells his story, the Chimera breaks into the Hub. The alarms go off. Rupert admits before he disappeared, he began a program to find drugs to suppress the alien DNA in the Chimera. He tracked down Ianto and Torchwood Three to access the Torchwood Mainframe to retrieve the recipe for the serum.
Ianto is disappointed that Rupert, whom he admired, lied to him. He goes to look for the creature on his own. When he finds it, it appears as a metal man and begins to strangle him. Rupert runs in and injects the creature with the serum. The Chimera fights back and kills Rupert in its death throes.
Ianto and Jack place Rupert's body in the vaults and wonder what legacy they will leave behind.
- Jack's coral can be seen sitting on his desk.
- Ianto's fear is a man made of metal, a reference to his ordeals with the Cybermen.