Feel free to explain how Quake 1's plot made any sense, given that it basically doesn't. As I said, it's just an excuse for portals between completely unrelated maps made by a group of people to connect together. Rather than bridge from one location to the next, you simply warp to a random place that the next map maker made.
In Quake 2, it's a simple plot, that follows a clear mission style structure, where you've penetrated the Strogg base and set out to help take down its defences and leaders from within, so the rest of the assault can get through.