Players retiring prematurely happens more than one might think. Rookie QB Eric Couch was one player who retired after signing a rookie contract and before a regular season game. He's still guaranteed all the bonus money that was promised him. Teams can in some instances, go after some of the signing bonus (as previously mentioned) through arbitration via the "Barry Sanders Rule".
Bonus money is just that, a bonus. It's extra money you promised a player to sign a contract with your team. How the league figures it into restricting the owners, known as cap, is not the players concern.
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Example: (GM) - "Hey kid, I think your pretty good.
(Kid) - Thanks
(GM) - What do ya think about playing for our team. I'll pay you $100 per regular season game. That's $1,600 per season and the league will even give you extra $$ per playoff game. Heck I'll do that for 3 seasons if you'd like. What do ya say kid?"
(Kid) - Well, I'll have to think about it.
(GM) - I'll tell you what kid. I'll give you $1,000 right now if you sign this contract on the table right here. It's yours to do whatever you want with it..
(Kid) - I can buy a car with it? Or give it to my mom?
(GM) - Sure kid. Whatever you want. It's yours. Just sign right here.
But you have to make the team to get game checks from us.
And we have to play in the playoffs for the league to give you those checks.
So kid, What do ya say?
(Kid) - What if I get hurt or can't play?
(GM) - We still pay you game checks as long as your on the team. And you can't be on the team until you sign right here. And I'm gonna give you an extra $1,000 just to sign right here.
(Kid) - Ok it's a deal.
(GM) - Great. Sign here and here's your $1,000. I hope you make the team. Good luck
Note: Obviously a dummied down example but you get the picture. The kid has to worry about making the team to get game checks and the GM has to worry about getting the kid signed and working within the cap restrictions set forth by the league and agreed upon by the owners.