In The Crucible, what choices does Mary Warren make that affect the outcome of her situation?
First, even though Mary Warren seems to understand the consequences of the girls' dancing in the forest and conjuring spirits, she never tells anyone in a position of authority. Though she initially told Abby and the other girls, "we've got to tell. Witchery's a hangin' error [....]! We must tell the truth [...]!" she is simply too cowardly to go against the group. Her decision not to tell essentially protected her from the other girls' wrath.
Next, Mary Warren does come clean to John Proctor after Elizabeth Proctor has been taken into custody as a result of Abby's accusation that Elizabeth sent her spirit out to attack her with a needle. She acquiesces to John's desire for her to go to the court and tell the truth, but her inability to stick to the truth -- her decision to, once again, save her own skin when it comes to the other girls -- leads to the continuance of the witch trials and the eventual deaths of many innocent people.
In some ways, Mary Warren's cowardice and her decisions to protect herself rather than her community render her even more responsible for the witch trials than someone like Mr. Hale. She knows, from the beginning, that the girls are lying; she knows, and she chooses to say nothing. She had the power all along to put a stop to things, if she'd have been brave enough. Her cowardice allows her to fade into the background of the story after the episode in the courtroom where she accuses John of being in league with the Devil. After her moment in the spotlight, Miller seems to say, she fades back into the scenery as just one more person who had the power to stick up for what was right and chose not to.