The tool is known as an orbitoclast. It's a specific medical tool intended for the performance of "transorbital lobotomies".
Warning: Gory
The implication is that Sister Sage has performed a lobotomy on herself. The Deep finds her sitting watching TV, eating snack food and generally chilling out, all things she would consider to be worthless activities if she still had her full intelligence.
SheNot to worry though. Her fact file says that she has a mild "healing factor"moderate regeneration", so we can reasonably expect that this is temporary and something she does semi-regularly.