According to Denny Glass, the Combine was the "stupid hippie name" for a kind of shadow government that actually ran the United States of America. Although he provided no better name for it, he admitted to Jessica Willamy that he in fact worked for them, starting sometime in or slightly before January 1967. Jess first believed that she had gotten separated from Denny because he had died — perhaps because he took Blue Moonbeams – but in fact he had been recruited by "the Combine".
During 1967, he worked on their behalf to spread Blue Moonbeams in the Haight. As a part of that plan, he was tasked with undercutting the Goblin's business in untainted LSD so that the demand for Blue Moonbeams would rise.
Because he confirmed the existence of "the Combine" to Jess, her life was immediately placed in danger. They would not let her live, so he urged her to immediately go on the run. She ran from town to town in the United States for decades afterward. At various points, they came close to killing her — ransacking her apartment in Houma, driving her into a corn field in Kansas, forcing her to live her life with her head constantly over her shoulder, unsure whether her paranoia was justified.
Eventually, sometime around the dawn of the 21st century, when she was living in a remote house in New England, "the Combine" caught up with her. Knowing she was about to be killed anyway, she placed a gun in her mouth and was about to commit suicide. As she tested the trigger, the TARDIS materialised, and the Fourth Doctor whisked her away from danger. Just before doing so, he confirmed that "the Combine" were indeed quite real and quite dangerous, producing a book by Jack Stimson — The Secret Government — as evidence. (PROSE: Wonderland)
Behind the scenes Edit
The name and indeed concept derives from Ken Kesey's One Flew Over the Cuckoo's Nest, which was an important work of fiction to the counterculture movement of the 1960s. In that work, the character of Nurse Ratched is the main personification of the Combine.
The difference in Wonderland is that the existence of the Combine is explicitly and undeniably confirmed by the Fourth Doctor. In Nest, it's a bit more ambiguous whether Nurse Ratched is behaving badly at the behest of an actual authority, or whether she's just an old battle-axe acting independently.