Mulder's line "This is America. Just because you get more votes doesn't mean you win" is a reference to the 2000 Presidential Election from a few months prior. George W. Bush received fewer votes but was awarded enough electoral college votes to become president.
This episode sets up the departure of Mulder from the X-Files. Writers Chris Carter and Frank Spotnitz decided to have AD Kersh deny him re-admittance as a way of phasing out David Duchovny's involvement, having established with the actor that he didn't want to return for Season 9. (Duchovny felt that the show had changed in his absence and had become more of an ensemble show, hardly surprising given that the main actor had decided not to come back for half the season.) The aim was to set up the storyline for John Doggett and Monica Reyes to take up the reins instead. Duchovny revealed that he was perfectly happy with this passing-the-torch approach.
Agent Doggett is told that to access the secret database, the password is three words; "Fight the Future." "Fight the Future" was the tagline of The X Files (1998).
This is the first time that Mulder and Doggett meet.
On his return to the basement office, Mulder says "Who says you can't go home again?" Home Again (2016) is the title of the fourth episode in the tenth season when Mulder and Scully are indeed back at the agency and back on the X Files.