You've played Doom, I hope, and you know that it is all about action: if you want more story or more plot depth or detail, you're out of luck. Doom excels at what it is, and Quake follows the same philosophy.
Quake's story line and setting amount to a meager few paragraphs in the Quake manual, nothing more than window dressing on top of the brutally simplistic "kill monsters, find key, exit level" style of gameplay. Once you've cleared a level of monsters, it's a desolate, empty place, much like strolling through the lot of a deserted Hollywood movie studio after the cast has gone home. Quake is clearly much more enjoyable as a multiplayer game.
On the contrary, Marathon 2 offers an intriguing, well-developed plot and story line that rivals some of the best science fiction currently on television. The player is given missions by Durandal, a hyperintelligent computer that helps plan out humanity's war against the alien Pfhor. The story can get overly complex at times, especially since the game refers back quite often to elements in the original Marathon, which is currently unavailable in Windows 95 format. (For more on the story line that connects Marathon and Marathon 2, check out the excellent Marathon's Story Web page, maintained by Hamish Sinclair.)
In addition to a more robust story line, Marathon 2 also has what Bungie calls "interactive civilians." During many game missions, you will be joined by computer-controlled allies--called BOBs--who can help you out in a pinch.
Quake gets points here for being totally immersive, but Marathon 2 wins this one by having a better story line, cool computer-controlled allies, and other single-player-friendly features.