In "Unrequited", she gave Mulder information on three generals who had allowed the US military to leave American POWs in Vietnam. She told him their names, which helped Mulder and Scully save one of the generals from death at the hands of a revenge-seeking veteran that had escaped from Vietnam.
In the episode "Zero Sum", Marita was contacted by Skinner. He had been involved in a cover-up of a death due to bees carrying smallpox. She urged him to tell the truth to the authorities.
We didn't see Marita again until the fifth season episode "Patient X". She showed up at the beginning of the episode as the leader of a UN recovery team. She had come looking for evidence of what happened at Kazahkstan, after a group of people had been burned to death there. She informed the Syndicate on Krycek's activities. Later, she confronted Krycek on ship and they kissed! Yay! She then disappeared with Dmitri, a boy that had infected by the black oil and was being used by Krycek as leverage to negotiate with the Syndicate.
In the same episode, Marita Covarrubias was attacked by Dmitri and the black oil. Her body was invaded by the black oil, and the Well Manicured Man's group of doctors tried to save her but couldn't, at least as it appears.
In season six Marita Covarrubias made a surprise appearance in Fort Marlene, but she was in bad shape, the victim of horrible experiments by the Syndicate, the group she had once worked with. They had apparently used her to test a vaccine against the black oil. Covarrubias was last seen with Krycek and Spender trying to get her out of Fort Marlene.