In the Season 2 finale, Preacher James and his congregation of the Returned descend upon the Langston house on a mission to stop Rachael's baby from being born. However, they are met by Bellamy, Henry and Fred, who are armed are ready to fight to protect this child.
A series of inexplicable events leads Bellamy to believe that Rachael and her unborn child are in danger; at the same time, Preacher James is predicting that the baby's birth will unleash an ancient evil; and Margaret rallies the Returned at the government facility.
Things turn more ominous in Arcadia with the return of Preacher James, who seems to have a strange and unnerving connection to Bellamy. Elsewhere, Margaret's presence is quickly felt at the government facility where she and other returned are being detained; and faith becomes harder to hold onto when the unthinkable happens to Henry.
The loss of a beloved member of the community leaves Arcadians in mourning; and a cure for the virus is provided by stem cells from Rachael's baby, but Rachael suddenly disappears and Bellamy and Maggie seek help from a surprising source. Meanwhile, Henry uncovers the facts about Margaret and his family's role in the fire at the factory.
Fear and anti-Returned rhetoric rises as the virus spreads; Bellamy and Sheriff Fred make every effort to track down the True Living members before they can do any more harm; and Maggie gets closer to finding a cure, but then a kidnapping and a hate crime bring her progress to a halt.
Rachael refuses treatment for the virus, fearing for the safety of her unborn child; at the same time, Elaine's brother Ray comes down with the disease. Meanwhile, Deputy Carl throws his support behind the growing anti-returned group, True Living; and Brian Addison takes more than a passing interest in Margaret.
A desperately ill Bellamy turns to his shadowy government contact for help and ends up learning something shocking about his own past; and the living seek answers after another returned vanishes into thin air. Meanwhile, a newcomer to Arcadia makes Henry an interesting offer.
Margaret proves she's a force to be reckoned with when, to her displeasure, Barbara makes strides in mending her relationship with Fred and Maggie. Elsewhere, Bellamy's situation grows more precarious as he struggles to keep his secret from Maggie, all the while taking desperate measures to deal with a strange virus that is spreading amongst the returned.
Margaret convinces Lucille to host a dinner celebrating Jacob's return, but the evening turns tense with the arrival of unexpected guests who end up putting a further strain on family relations. Meanwhile, Bellamy continues to research the history of the mysterious bones; and Rachael receives unsettling news about her baby.
Bellamy confides in Tom, explaining that he's one of the returned; at the same time, the pastor senses a need for a new parish specifically for those who have come back to Arcadia. Elsewhere, Margaret seems determined to keep hidden whatever connection the Langston family has to old human bones that have mysteriously turned up in the river.
Bellamy and Sheriff Fred fear that Caleb may have returned to Arcadia when they hear reports that someone is living in his old hunting shack. At the same time, Bellamy struggles with the knowledge that he is one of the returned and has difficulty following the orders of his mysterious boss. Meanwhile, Janine tries to save her marriage to Pastor Tom by moving back home; and Margaret Langston is none too happy to learn what has become of the family business.
Season 2 begins with Bellamy facing another shocking turn of events when he awakens alone and abandoned at Arcadia's outskirts unable, at first, to account for a week of his life. As his memory returns, the town welcomes back from the dead powerful matriarch Margaret Langston after more than a 30-year absence.