A training buddy of mine plays football for his university and tore his ACL. After successfully completing rehab he got back into lifting and last week I saw him squat 660 lbs for a PR.
Teach yourself how to low bar squat correctly. It is the king of all exercises. Download the eBook version or buy the paperback of Mark Rippetoe's Starting Strength. It has the most detailed instructions on how to correctly perform the big four barbell exercises (Low Bar Squat, Deadlift, Bench and OHPress) and not to mention some incredibly useful details on programming when it comes to novice lifters.
On Mark's forums you'll find plenty of athletes from various sports including combat sports; many who have come back from serious injuries. There's one guy on there who fell off a roof and landed on the hard pavement on his feet and shattered both his legs completely. After years of rehab and a little bit of coaching/consultation from Rippetoe himself- the guy was lifting some major
weight at local powerlifting meets in his hometown.
Mark Rippetoe himself, has no ACL in one of his knees and squat some heavy
weight considering his age.
Starting Strength is not just for PowerLifting, like I said all types of athletes have benefited from the program when done right.
If you have a tablet, I seriously recommend buying the eBook version- it is pretty cheap.