Upon arriving in Salem Village, Alden knew nothing of the troubles of Salem but rather had the misfortune of having his son, also named John, taken as part of the prisoner exchange. Due to his father having been accused of witchcraft, and thus unable to return to Quebec to bargain, John Alden IV was taken to the Bastille in France, from whence he would not return for almost a decade. Alden also didn't know that one of the accusers, one of the "afflicted", was Mercy Lewis. She was orphaned in the latter half of 1689 in Casco Bay, Maine, during a raid on her village. Historians have speculated that she had an ulterior motive in accusing Alden, a desire for revenge on those she felt had failed to protect her family. Alden's second wife, Elizabeth, had ties to Maine as her father was a wealthy lumber merchant, a business he inherited through marriage. He was a perfect target. He was subsequently accused and convicted of witchcraft during the Salem witch trials in May 1692. At the time of his trial, Salem jail was already full and so he was carted off to Boston. In the coming weeks of incarceration he had been inclined not to make much of the matter, but was prevailed upon by some friends and broke out of jail, fleeing in the night on horseback. It was mid-September and his decision to run away proved wise, as evidenced by the fact that Giles Corey was crushed to death within a few days of his departure. Per some sources it is said he escaped to New York, but more likely Alden escaped south to Duxbury, his hometown in his youth and the location of many of his relatives, namely his younger brothers David and Jonathan and a very large amount of nieces and nephews still living in the town. According to the oldest traditions, when, having awakened his family in the dead of night and causing much alarm, he said in a terrified voice that he was "flying from the Devil, and the Devil was after him!!"