Here, this pretty much sums it up quickly. TC comes before AP story-wise, and AP before X-Rebirth. TC and AP are at heart sandbox sims, but there are plot lines you can engage in, that continue the X universe story (and I would most definitely encourage you to do so) by giving you missions to complete as you pick up and engage in the x universe story. Personally, I would recommend starting with TC first, then play AP afterwards. They are actually two separate games, and AP does not "automaticalyl" start after TC...as a matter of fact, you decide when TC ends (usually after you've done all the plots, and built up your empire to a point you are a major force to be reckoned with, and if you desire, can go reek havock on some other race for fun, or whatever reason you want to. It should be noted that there are mods that you can use, if desired to install all the major plots from TC into AP and play that way, if you don't wish to play both at some point.

Ohh, there is only one manual, because it really covers the basics of both games. I believe AP was originally an expansion to TC.

Others will probably drop by and give you a more eloquent explanation then I have, but that's my take. Have fun whatever you decide, and there are quite a few folks who are playing now, or have played a lot and monitor this game forum if you need help down the road.