Instructions
Build anti-aircraft buildings, such as missile turrets and photon cannons, around the perimeter of your base. These buildings may cost some of your resources, but they can provide a great first-line of defense for your base when defending against Carriers.
Build aircraft that specializes in anti-aircraft, such as the Viking. Your aircraft will still be vulnerable to the Carrier, but they will have an increased amount of mobility that they previously did not have when combating the large ships.
Manually control your units when you are fighting the carriers. By default, your ships will automatically begin shooting the smaller, weaker ships that deal damage for the Carrier. In reality, it is much faster to manually attack one of the Carriers and destroy it. Once it has been destroyed, all of its smaller planes are destroyed, too.