Cassandra Spender was something of an embarrassment to her son, because she believed she was abducted by aliens
and was very vocal about it. At one point she even joined a UFO cult. Jeffrey believes that
she brainwashed him, as a child, into thinking he'd seen her being abducted.
Though Cassandra was disabled and couldn't go anywhere on her own, Consortium agent Quiet Willy took her to Ruskin Dam in Pennsylvania where former abductees (including Scully) were gathered. Though all the other people there were killed or left for dead, Cassandra was abducted again, lifted into the sky in a beam of light. Her abandoned wheelchair was the only evidence they found of her.
Though Jeffrey thought his mother was crazy and feared she would hurt his career, it's clear that he loved her very much. He was very protective of her, and was quite upset at her disappearance. Not believing in aliens, he blamed Mulder and Scully for what happened. He was convinced that if they hadn't encouraged her "delusions," she wouldn't have gone to the dam.
She was gone for over a year. When she was finally returned, she no longer needed her wheelchair. The Consortium had been made her into the "perfect hybrid," the one whose existence meant the end of the human race. And she no longer believed that the aliens were benevolent.
The scene where Jeff is reunited with Cassandra is one of the most poignant in the whole series. "You've been gone so long I thought I'd never see you again," Jeff says. "Don't cry, honey," Cassandra replies...but she won't tell Jeffrey what's happened to her. Instead, she wants to speak to Agent Mulder - which obviously hurts Jeff.
It turns out that Cassandra knows Jeff has fallen under the influence of his father, her ex-husband - CSM. That is why she won't confide in him. And by the time Jeff realizes that his mother is right, it's too late: Cassandra has been taken to the hangar where the alien rebels wait, and is burned to death, with most of the Consortium and their families. Jeff is motherless again, this time for good.