Welcome to middle school! I've seen four kids through this transition, and every single one of 'em went through a phase just like what your son is experiencing. Even my youngest, who is as smart as they come and was an excellent student all through elementary school, is struggling this year (he too is in 6th grade). He tells me he did his homework at school, then has missing assignments noted on his report card. I get phone calls from teachers wondering why he didn't turn in his big project, and of course he never tells me about these things until 8 PM the night before it's due and then flies into a panic because we don't have the stuff he needs for it. AAAAAAAAAAAARRRRRRGH!!!!!!
Still, the only one of my kids who never fully recovered their "drive" was my 14 YO son, and even he does well in the subjects he's interested in. I'm no expert, but I think a lot of the difficulties kids have at the 6th grade level come from their immaturity......they're just too young to be in a junior-high environment, and it tends to overwhelm them. Back in the dark ages when I was in junior high, it started at the 7th grade level, which made more sense, and I think it's just nuts to put little kids in with fast-growing, sexually maturing 7th and 8th graders.
Anyway, you need to talk with your son---not AT him, but with him. Find out, if you don't know already, who he hangs out with at school; maybe he's running with a different crowd, or having difficulty even finding friends. Ask him what subjects he's having trouble with, whether he likes his teachers, and what goes on in class, as well as in PE and at breaks. If you don't like the answers, find out who, what, when, where, and why!
Above all, don't threaten him. He's already going through the roughest part of adolescence, and everything he thinks he knows about himself is changing. Be firm in insisting that his schoolwork be a priority, and of course, you'll want to talk with his teachers on a regular basis; but try not to be punitive........believe me, there'll be battles aplenty during the next 5 years or so, and you don't want to feel he HAS to defy you in order to gain his independence. (This is how kids end up making horrible decisions about sex, drugs, and other matters of importance.) And whatever you do, DON'T threaten him with anything that you aren't willing to follow through with, or anything you have no actual control over, such as being held back. These days, almost nobody is held back; last year, my 14-year-old failed all his classes except PE and art, and they still promoted him!!
The other thing is, you need to assess whether he may be depressed. It's surprisingly common at this age and tends to be situational, but it should be addressed anyway if you even suspect it.
Good luck to you. I hope this helps.