Brennan's mother had been missing for 15 years when her remains appeared in the season 1 finale.
Her remains were located in 'limbo' the Jeffersonian's storage for bones that have yet to be identified.
When Brennan and the squints investigated the remains of Ruth Keenan they found that she had been hit across the head as a glancing blow (as if being pulled away just in time) which caused a slight mark on her skull and the subdural hematoma that, over time, had caused her death in 1993.
The blow to her head was caused by a captive bolt stunner of the kind that is often used on pigs. This is one of the clues that help solve the murder of Brennan's mother.
We later find out that Ruth Keenan was killed by hitman Vince McVicar. McVicar was part of the same gang of bank robbers that Brennan's parents used to be in.
After the incident with McVicar Ruth Keenan lived for another year, unaware of the bleeding in her head. When she eventually died, Max Keenan laid his wife to rest near 'sunset cemetary' where her remains were found and eventually brought to the Jeffersonian.