I had a nuke and my partner had a anti nuke. I launched my nuke at him cause we already won the game. And the anti nuke did not shoot and i killed his base. So anti nuke only fire at enemy nukes.
Well you wouldn't want to nuke the enemy and your partners base be in between and shoot down your nukes would you? Anti-nukes are activated when a nuke comes in range, not if the nuke is targeted near them. This makes it so that you can have anti-nukes around your base and keep the middle safe also. Long story short, it works best this way.