In an American prison child killer Oswald Danes is given a lethal injection but fails to die. CIA agent Rex Matheson is one of several severely injured hospital patients who should be dead but survive. The phenomenon is worldwide and the press dub it Miracle Day,when noone dies. Rex's colleague Esther Drummond attempts to contact the long disbanded Torchwood and is visited by Jack as a result. The pair survive an attack by a bomber - after Jack - whilst the bomber, though blown to bits,goes on breathing. Gwen and Rhys Williams are living in seclusion in Wales with their baby when Gwen's old colleague Andy tells her that her father Geraint is one of the sick people who cannot die and that the world will be over-populated in a matter of days. Rex and Jack arrive in Wales to bring Gwen back to the States with them.

Rex brings back Jack and Gwen to Washington. At the CIA office Esther realizes that the rendition is being sabotaged from within the organization. On the flight home Rex unexpectedly needs help from Dr. Juarez to get the team safely on the ground. In the meantime the medical community tries to cope with the new reality of non-death.

Rex forces his boss Friedkin to confess that, in setting him up, he was obeying orders from a mysterious source. By confiscating his phone Rex's investigations lead to an empty warehouse belonging to Phi-Corp,a global pharmaceutical firm,containing vast amounts of pain killers. Rex's wound reopens and he seeks medical help - and more - from Vera Juarez,who has been invited by Jilly Kitzinger to attend a Phi-Corp meeting. Vera takes Gwen and they hear the announcement that all pain-killers will legally be dispensed without prescriptions in future. This is endorsed by Danes to popular approval.

The new Torchwood team travels to California intent on launching an assault on Phicorp. Dr. Juarez tells Rex where he could get his hands on drugs, no questions asked. Torchwood's plan to steal data from the pharmaceutical giant does't quite go as planned. Meanwhile, health planners are looking to new facilities dedicated solely those who should have died but are still alive. One of the participants describes it as an old style plague ship. Jack puts a permanent trace on Oswald Danes so that he'll always know where he is. Danes has been doing his own research on Phicorp and is convinced they are under the control of someone or something that is doing a very good job hiding their interests. He also finds that he has competition for the limelight.

Gwen heads back to Wales when she learns that her father has been transferred to one of the new holding camps. She has every intention of getting him out of there, but the military is in charge and they're proving to be more than a bit uncooperative. Back in the U.S., a similar camp has been opened in San Pedro. Along with the camps, governments around the world have adopted a classification system to ensure that those who should be dead, Category 1, are sent to the camps. This is all too much for Dr. Vera Juarez who travels to California to join Torchwood. Posing as a patient, Rex goes to the San Pedro facility while Vera gains access as a medical inspector. They cannot believe what they learn.

Knowing exactly what happens to Category 1 patients in the overflow camp, Rex uses a video recorder to document what is happening. Esther knows that something has happened to Vera Juarez and tries to learn more from the camp director, Colin Maloney. Jack meanwhile introduces himself to the Chief Operating Officer of Phicorp, Stuart Owens, who says that Miracle Day is something far greater than just his company. He suggests that Jack search for something called the Blessing. Having successfully rescued her father from an overflow camp in Wales, Gwen returns to Los Angeles but learns on arrival that her entire family has been kidnapped. The ransom: turn over Jack Harkness.

Gwen has decided that the only way to save her husband, daughter and mother is to deliver Jack to the kidnappers as demanded. She's taken Jack prisoner and tells him she's convinced that it was something he did in his past that is at the root of miracle day. In flashbacks, we learn that Jack came to America in 1927 on a Torchwood mission. He befriends Angelo Colasanto and they are soon involved with bootleggers. When Colasanto realizes that Jack is immortal he takes him prisoner, subjecting him to repeated deaths only to have him revive. When Gwen delivers Jack as ordered, it's obvious that those earlier events are in fact the key to what is happening in the present.

Jack and the others are taken to Angelo Colasanto's home. He's now a comatose old man but his granddaughter Olivia assures them all that he is not responsible for miracle day. He has however kept himself alive in large part because of Jack and has followed his exploits with interest over many, many years. He's not however responsible for miracle day. Olivia tells them of the three families - named Ablemarch, Costerdane and Frines - who are. Now back in the CIA fold, Rex doesn't quite realize there is a spy in their midst. Jack does however discover something interesting in Colasanto's home. In Texas meanwhile, Oswald Danes is preparing for a rally but isn't prepared for the news that governments are preparing for a new category of individuals to deal with people just like him.

Two months have elapsed. Back at CIA headquarters, Rex is making progress trying to track down the three families. References to them are few and far between but he soon begins to think that there is a mole in the CIA. After her deportation back to the UK, Gwen has been working at keeping her father hidden from the government agents responsible for rounding up all Category 1's. Esther and Jack are hiding in Scotland while he recovers from his gunshot wound. They are all soon reunited and even Oswald Danes, also on the run, turns up. Collectively, they soon discover a connection in two places, Shanghai and Buenos Aires and set out to find the source of the Blessing. Jilly Kitzinger is already in Shangai having been drawn into the secret families.

Jack, Gwen and Oswald Danes are in Shanghai with Rex and Esther in Buenos Aires. They are at opposite ends of what proves to be the Blessing. The Families interest in getting rid of Jack is revealed as is the origin and meaning of miracle day. They realize that bringing miracle to an end will have a cost as some of those who have survived will most certainly die. Jack, the only remaining human, shows himself more than ready to sacrifice his life if that what it takes to end it all. One member of Torchwood will not survive.