Re: Basement of the server complex
They lead to another series of levels that are only part of the PDX storyline. Conversely, the part of the complex that you're doing your current mission in is not available in the PDX storyline.
No, that area is not tied to any main missions, it's all for exploration (though it does involve a small side mission). Also, I don't think that parking basement entrance takes you where you think it'll take you.