" There is news, sir, that the court--the court must reckon with. My niece, sir my niece---I believe she has vanished"

This quote pretty much is clear on what it means, Abigail had fled Salem shortly after John Procter had been arrested sentence to be hanged for witchcraft. She also realized  that the town did not like the idea of the fact that Rebecca Nurse, and John Procter, the two honest and good people in the town were going to be hanged so she knew that the court was going to turn on her so her and mercy had fled Salem so they wouldn't be caught.