Perfect Dark.
Arguably the best FPS ever made in it's time, no history-the FPS I've ever played. Graphics are still pretty decent, but frame rate suffers. Heck the N64 was barely able to run the thing, Goldeneye 007 pushed the N64 to it's limits already. But this can easily be overlooked for the excellent level designs, unforgettable moments, weapons, multiplayer, and characters. The second best game I have ever played only behind Ocarina:
The storyline is one of a kind-or at least I enjoyed it. Basically, a future mega corporation called Datadyne is working with an evil alien race called the skedar to use an alien megaweapon in the bottom of the pacific to destroy their nemesis race, the Maians and unknowingly to Datadyne, plan to test it on Earth, which will destroy it.
The Maians, the friendlier and good race, are sided with the Carrington Institute, who rival Datadyne. You are Joanna Dark as you eventually unravel the plot and stop it. You ultimately end up in the Skedar homeworld and take out their leader.
In the end and in irony, it is aliens with technology light-years ahead of humanity that calls upon them to help fight the skedar and prevail.