Yes I would agree with everyone else here, all I hear is the focus from you for your wife to be happy.
That's admirable but kind of out of place.
It's probably what caused alot of this problem if I may be so bold to say so.
You have probably never asked for anything, you've probably done everything & anything to make her happy - all at your expense. The "nice guy" syndrome - it doesn't work.
When you show that your needs/wants are important without being a baby of course, you communicate that you are important, you communicate that you have value, you have self-respect, etc.
Currently you communicate that everything is ok.
It's ok that your wife had thoughts of having an affair. It's ok that your wife travelled to a vacation destination without you with some other man. It's ok that your wife had an affair. It's ok if your wife takes your kid away (she can't by the way, just so you know).
It's all ok because you're ok with that.
That's kind of boring and isn't very attractive.
Time to be a little assertive, you're a man, you have a pair, own them, stand up for yourself.
What she has done isn't ok.
Seriously bro, you invested all this time & energy into your wife during all of these periods of her depression, you took care of her every request and made sure she was taken care of and now that she walks all over like you're some doormat, you're ok with it.
I have to question something, are you really OK?
Make it known that she can't take your son away from you, you want joint custody and will do whatever is necessary to get joint custody. Heck, push for full custody - you can get it, she has a history of mental instability & depression - the courts don't rule what's favorable for the spouses during this event, they care what's in the best interest of the child. Removing the child from an environment which including a loving father (aka YOU) and travelling so far away to make you a distant memory wouldn't be in the child's best interests. Please don't agree with any of what your wife wants.
If she really wants out of the marriage and there is no chance in getting her back, it's really time for you to take inventory of your life (it's probably been a while) and start determining what you want in your life. Don't be afraid to ask for whatever you want - you're allowed, it's your life.
No more doormat behavior either. You don't have to mean or angry, you just have to stand up for yourself and tell her that what she is doing is not good for you or your kid and you will start taking care of your needs first and she can start fending for herself - you've cared for her long enough and were rewarded with this.
Stand up for yourself, no one else will do it for you.