Mulder: But you saved me! As difficult and as frustrating as it's been sometimes, your goddamned strict rationalism and science have saved me a thousand times over! You've kept me honest. You've made me a whole person. I owe you everything, Scully, and you owe me nothing.
Mulder going to Antarctica to save Scully from the spacecraft, bringing the antidote for the virus. Awesome Moment if there ever was one in all the films that ever were made. His giving her some layers of his clothes and his thick socks was great as well.
Scully's speech at the end of the movie, explaining why they should continue with their work on the X-Files as long as they are allowed to do so. It implies that they are looking for the truth so that they can help people, which, after all is their job as FBI agents. This might however save the planet, too, no less.
Scully: I can't [quit the FBI and be a doctor]. I won't. Mulder, I'll be a doctor, but my work is here with you now. That virus that I was exposed to, whatever it is, it has a cure. You held it in your hand. How many other lives can we save? Look, if I quit now, they win.