In the wake of Judas' betrayal and the crucifixion, the eleven remaining disciples flee to the Upper Room where, only days before, they had happily gathered together for the Last Supper ("Walk Away"). Once treated as minor celebrities, they are now hunted by both the Romans and the mob. Thaddeus is carried in, broken and bleeding, after being stoned. Everyone is afraid and they all blame and fear each other. ("Anyone But Me"). Fighting breaks out between them over how and or even if they should continue even as they long for the old days. ("Do You Remember"). Simon, who claims to have murdered Judas in revenge for his treachery, argues for a violent response to their loss. ("Pick Up The Knife"). Peter, their supposed leader, cannot get past his own betrayal ("Three Times").
Mary Magdalene arrives. A controversial and unpopular figure simply because she is a woman, most of the men shun her. Jimmy loves Mary and secretly wants her to run away with him ("Magdalene"). Although tempted, she refuses. Her first loyalty is to their Teacher and his legacy. She challenges the others to find their courage ("I Did"). Her beliefs are in stark contrast to the doubt of Tom, who now cynically disparages their former life as nothing but a show. ("Give Up"). Mother Mary arrives. Almost out of her mind with grief and shock, she is come looking for her son, unable to comprehend that he is dead. ("Rain") She leaves them with the painful challenge – what will you do now? For that, they have no answer.
In the darkness, dogs howl and the world shakes as if it had broken in two. Bart wakes up from a dream of the past which he shares with his close friend, Phil. ("Sweet Dreams"). Thaddeus recovers but is haunted by his own terrifying dreams which he refuses to discuss. Mary Magdalene returns in great excitement. The tomb is open and the body is gone! ("Empty"). The men are frightened and confused. What to make of this? For Mary and Peter, it can only mean one thing – He has defeated death. ("What If?") One by one the disciples come around ("I Am Not Alone"). Only Tom remains unconvinced.
Without tangible proof, Tom refuses to believe. After all, why would such a great man choose nobodies like them for such important work, and why, if he was so powerful, would he have allowed himself to be killed? ("I'm No Hero). Most of the disciples are for letting Tom leave but Peter feels that it's important they all stay together. Tom challenges him to a "duel" – convince him and Tom will stay; but if Peter can't convince him, then they must all give up this delusion. The stakes are high but Pete accepts.
As he struggles to reach Tom, Pete realizes that they were chosen precisely because they were ordinary men. That is the hope they represent. And that it was His unconditional love for mankind that informed everything that He did, including dying for them. ("Ordinary") At the heart of Tom's resistance is his own shattering grief. ("Why") Through Pete and the others, Tom finally comes to understand that what truly defines their Teacher as miraculous was the message he preached: all men should love one another. With this realization, Tom makes the decision to join the others. ("Rise Up")
As they prepare to leave the room, Thaddeus cuts short their new found resolution by revealing his earlier "nightmare." It was a true and terrible vision of their eventual fate -- if they leave to preach this new word, all of them will die horribly. Peter finally assumes the leadership he was destined for as he sings of his own calm acceptance of such a death. ("Now I Lay Me Down to Sleep").
In the end, they all decide that no matter the consequences, they will continue on together. They ask Mary Magdalene to join them as an equal and when she does, they are once again twelve ('Our Love"). Their fears have not been banished but they are all now bound by this renewed love and faith in one another. They are now ready to leave the room and face the world ("Rise Up – Reprise").