R55 just cranks- doesn't fire

[snydermr2]

I have a 2010 Mini Clubman S. Recently the alternator was going bad. I attempted to make it to / from work one last time by charging the battery all the way up the night before. Made it to work, but didn't quite make it all the way home, and ended up pushing it to a parking lot. I took the battery out, took it home leaving the car at the parking lot, and charged it up overnight. Took battery back and reinstalled it the following morning thinking I could start it and drive it the last couple miles home, but all it would do was crank and crank. Wouldn't fire. Once in a while I'd get a partial fire--like it wanted to fire.

Had it towed home. Kept trying to figure out why all it would do it crank--and it cranks fast like normal, just won't start. I gave up, went ahead and replaced the alternator, put it all back together, but it still only cranks.

Any ideas on what I could have done to it driving it that one last time and didn't make it quite home? Other than the alternator going bad, it ran fine before. Could that have done something to the fuel pump? Or maybe I blew some fuse or something somewhere?