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 no-one 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 quartet escape to Los Angeles and attempt to enter the Phi Corp headquarters but they have been followed, by a man who claims to know Jack from long ago and believes he holds the key to Miracle Day, though he is killed by Rex. A right wing housewife Ellis Hartley Monroe achieves fame with her Dead Is Dead campaign, which involves herding the sick into ghetto hospitals. Danes, sensing that he will be eclipsed by her celebrity, publicly opposes it to general acclaim. However Gwen learns that her father is to be put into one of these 'overflow camps' for the sick, back in Britain.

Dr. Juarez joins the new Torchwood after category guidelines are released for patient care. Esther and Rex go undercover to find out what is happening to Category 1 patients being sent to 'Modules' at overflow centers. Meanwhile, Gwen flies back to Wales to remove her father from an overflow center. Dr. Juarez manages to use her credentials to enter an overflow center as an inspector while Jack attempts to convince Oswald Danes to expose Phicorp.

Jack confronts Stuart Owens, PhiCorp's chief executive, who admits that he is as ignorant as everybody else as to the reason for Miracle Day. All he can tell Jack is that the answer should be in a cryptic document, the Blessing, which originated in Italy. Rex learns that the California overflow camp incinerates the 'undesirable' sick - illegal immigrants, criminals - and Vera. Rex and Esther are caught by Maloney but are saved by Maloney's appalled aide, Ralph, who shoots his boss and helps them escape. Gwen springs her father from Cowbridge but on return to America gets a call to say that her whole family has been captured and will only be released if she helps trap Jack.

In Ellis Island, New York in 1927, Jack meets a young Italian immigrant Angelo Colasanto. They become lovers and boot-leggers, working for a gangster. Together they uncover a plot to kill Franklin Roosevelt though Angelo is puzzled by Jack's immortality, following a shoot-out. As a result he is coerced into an unsuccessful attempt on Jack's life. In the present, Gwen is taking Jack, her prisoner, back to Wales when they are attacked but saved by Esther and Rex. They are then summoned to meet Angelo.

The team is taken to see Olivia Colisanto, in whose house her grandfather, Angelo, ancient and comatose, lies on a life support machine. She explains that in 1928 three mobster families, named Ablemarch, Costerdane and Frines, tapped Jack's blood to gain immortality - the Blessing. Those families have now disappeared but seem to hold the key to Miracle Day. Angelo dies, baffling new CIA boss Shapiro, who deports Gwen. Jack finds a link between Angelo's death and a plate containing a mysterious force field under his floor. He gets Esther to take it and him to safety whilst Jilly tells Danes that he is expendable.

Whilst the CIA look in vain for traces of the three families, Esther somehow gets Jack to Scotland,from where they join Gwen and her family in Wales - as, rather surprisingly - does Oswald Danes, claiming he wants to be helpful. He has stolen Jilly Kitzinger's computer, which shows her to be going to Shanghai. After the police have raided Gwen's house and taken her father she sets out with Oswald and Jack to Shanghai, where Jilly is meeting a woman called Mother Colasanto. Esther and Rex pursue a lead in South America.

An underground bloodline flows from Buenos Aires in South America to Shanghai, where Mother Colisanto shows Jilly that she is planning to blow up her hide-out whilst the Blessing maintains its immortality. In Buenos Aires an explosion kills Rex and Esther's army escort, as they become aware of a CIA mole whom they allow to believe they are dead. They are nonetheless caught and taken to the South American lair of the Mother's cousin, where the other half of the Blessing is kept. Gwen, Oswald and Jack infiltrate the Shanghai hideaway where they learn how the families, using Jack's blood, attached it to a force field to give them immortality but how the aliens misunderstood and recently gave immortality to the Earth in the spirit of benevolence. Sacrifice and redemption on two continents lead to the destruction of Miracle Day with the capture of the mole and the restoration of order. For one of the survivors there is an amazing discovery.