If your Apple TV box is black and 3.9×3.9", then it is at least 2nd generation.
Identify your Apple TV model - Apple Support
If your Apple Remote (aluminum) got unlinked for the Apple TV box, then you can re-link it as described. Do both steps: the unlinking and linking.
If your Apple TV remote isn't working - Apple Support
If you need a replacement for a broken remote, then you can buy one. You may have to link replacement remote as described above. Buy an Apple Remote (aluminum) - Apple TV accessories - Apple Store online
If you want to use the software remote on iPhone with an older model Apple TV box, then you may still need the physical remote to help set that up:
The Apple TV (3rd generation) needs a functional remote to set up the Apple TV Remote widget in Control Center.
For the Apple TV (3rd generation), your options are:
The Apple TV (2nd generation) is not compatible with the Apple TV Remote widget in Control Center.
For the Apple TV (2nd generation), your option is: