It depends more so on the controller. If its a newer controller or an elite one. They may take it. But there protocal is basically to plug the controller intona system. And if its not picking up. 9 times out of 10 they wont take it.
They mite take it if it can be fixed and give you a small amount of store credit
When you go to GameStop depending on the condition they will give you some money off of your next controller
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