In Act IV of The Crucible, Abigail and Mercy flee because Abigail can no longer have what she wants, John Proctor. The ony reason that Abigail got involved with the witch trials was to find a way to get rid of Elizabeth Proctor. Her goal was to free John Proctor of his current wife, so that she could become his wife.
Once Abigail sees that John Proctor is to die for being in league with the Devil, Abigail realizes that there is nothing left for her in Salem. She also senses that the tide will soon turn against the girls who have, through her leadership, given false testimony in the court, which results in the deaths of innocent people accused and found guilty of witchcraft.
"Parris informs the investigators that Abigail has taken money from his safe and left town. He fears rebellion among his congregation, only a few of whom came to the church to hear John Proctor's excommunication."
Both Abigail and Mercy are afraid of the retribution that will come to Salem in the same way that it came to the town of Andover. They are both afraid for their lives, so they run away.
"Parris: Excellency. it profit nothing you should blame me. I cannot think they would run off except that they fear to keep in Salem any more. He is pleading. mark it sir, Abigail had a close knowledge of the town and since the news of Andover has broken here.' (Miller)
The town of Andover is located near Salem, during the witchcraft hysteria in Salem, similar situations erupted in Andover, however, the people of the town objected to the proceedings that were finding respected people of the community guilty of witchcraft, so there was an uprising against the court and its officials. The uprising among the people against the court ended the witchcraft hysteria in the town of Andover.
If the same events took place in Salem, an uprising of the people against the court and its officials, Abigail and Mercy would be right in the middle of it. As experts on witchcraft and having given false statements to the court, they would be tried and probably hung for perjury.