I see you are in the Seattle area. There are some excellent spine doctors that you should be able to rely on to help alleviate your son's pain.
Be sure he is going to a fellowship-trained orthopedic spine surgeon (not a general orthopedist) or a neurosurgeon who devotes most of his time to issues of the back and neck, rather than to the brain. I would agree that you should get at least two opinions, perhaps one from the ortho spine doc, and one from a neurosurgeon in a different practice...and perhaps a third, if there is a discrepancy in diagnosis or how they would treat.
When the disc looks dark or black on a MRI, it is a sign that the disc is degenerating and is not healthy. The surgeon may need to remove a portion of it if it is pressing on a nerve.
A procedure on one level of the spine should be able to be accomplished without causing problems in adjoining segments. If it returns your son to an active lifestyle, it might prove to be the healthier option, as it sounRAB like he isn't able to do much the way things are now.
Welcome to the board. Please feel free to ask your questions as they come up. I know it is overwhelming at the beginning, but you will learn as you go along.
If your son does have surgery, it is entirely possible that he will feel better immediately. This can be dangerous as the tendency is to do more than the surgeon is allowing at the beginning. There is a healing process that is very important to the over-all integrity of the spine, so that he will not develop problems down the line. You will need to make this clear to him, so he doesn't get carried away and do too much too soon.
It doesn't sound like your son's problems are going to go away on their own...or that time is going to resolve the issues. Do your research and be sure you have found the best surgeon for your son's neeRAB. When you are convinced you have found the right person, then I think you will be comfortable moving ahead.
There is a book entitled Do You Really Need Back Surgery?: A Surgeon's Guide to Neck and Back Pain and How to Choose Your Treatment by Aaron G. Filler. You can find a used copy online for about $5.00. It is the best book I have found, and I own an entire library by now! It covers almost all topics -- anatomy, various back problems, descriptions of various imaging and tests, treatments, and various surgeries. There is a glossary at the back. If you are the type that enjoys reading and doing a little research, this book will help you talk to the spinal specialists, and understand what they are recommending for your son.
Good luck. You are a wonderful father to be helping your son. I wish you both the best.