She had an affair with the squire of the village, Claude Portillon and had twins, Lucern Portillon and Finicia Portillon from him. To conceal their illegitimacy, Agnes and the squire pretended that these were the squire's children from his wife, who died giving birth. This story has backfired when Agnes was exiled by the citizens to Sutherland's Meadow for not saving the squire's wife.
Her healing prowess was in large part due to her ability to channel Odic energy. In particular, she could see silver ships in the sky, called the Eighth Doctor the "Lord of Time" and knew that he had two hearts.
Because of her gift, she was hunted down by two Varaxils, "Lucern" and "Finicia", who took form of her children. At the same time, she was accused of being a witch and tried by John Kincaid, the Witch-Pricker. To save her and himself from being burned alive, the Doctor persuaded her to demonstrate her gift to the Varaxils.
What the Doctor did not expect was for the Varaxils to try to kill Agnes because of her gift. Due to an intervention by John Kincaid, she was transformed into a witch after absorbing all the Odic energy stored in the Varaxils' WitchStar. Not being able to control so much energy, she started attacking everyone around her, wounding the Varaxils and killing many villagers and Witch-Pricker's soldiers. In this state, she was impervious to both human muskets and Varaxil WitchStar. She followed the Doctor and Kincaid to the Varaxil ship at Vetter's Tor. There she killed the Witch-Pricker, who dared to openly confront her, but was then persuaded by the Doctor to step into a Lokic containment web.
The Doctor has managed to modify the containment web so that Agnes herself could freely walk away but all the Odic energy, hers and absorbed from the WitchStar, remained within the web. This residue Odic wave form was buried in a well for 350 years and kept some of Agnes's memories. Agnes herself left Tranchard's Fell to live in some other village, where she would continue being a healer even without her gift. (AUDIO: The Witch From the Well)