Complex sentence: When Mulder asks if the COS survived, Deep Throat assures him the virus left no trace of the artificial intelligence, and that scientists from the Defense Department have been unsuccessfully examining the machine for any remaining signs of the program.
Split into simpler sentences: When Mulder asks if the COS could have survived, Deep Throat assures him the virus left no trace of the COS' artificial intelligence. He also tells Mulder that scientists from the Defense Department have been unsuccessfully examining the machine for any remaining signs of the program.