There are eight fortresses to conquer in Air Fortress. Each fortress follows the same flow.
Fly to the fortress entrance
After being presented with the fortress progress screen, where you can see how many fortresses you have cleared and how many remain, you will begin flying over the surface of the fortress on you Lightspeeder. As you fly, the fortress will send a variety of flying combatants to attack you as you make your way to the fortress entrance. Along the way, you will also encounter a variety of platforms and obstacles hovering above the fortress surface. Energy and Bomb item capsules are also present and available to be collected. Do your best to collect as many of these as you can, as they will be a substantial help to Hal when he enters the fortress, but do not put yourself at risk to collect them. In addition to the prearranged capsules, it's possible to collect even more capsules from defeated enemies. Sometimes you will earn more energy and bomb capsules, while other times you might find exterior-only capsules such as the Shield and Crash capsule. Use them both effectively to increase your chances of surviving and reaching the fortress entrance. Your Lightspeeder will not survive any collision, and you only get three of them. Note: In the Japanese version, if you crash your Lightspeeder you must start from the beginning of the stage, unlike the American version which allows you to continue on by re-spawning your ship from the location you crashed.
Destroy the fortress core and escape
Once inside the fortress, you play with a new set of rules. Hal's survival is pinned to his supply of energy. Every move and attack that he makes will drain some of his energy. However, all of the energy lost through movement and attacks can be regenerated by standing still. Energy lost through collisions with hazards, enemies, and their projectiles does not regenerate, but Hal can occasionally pick up Energy powerups dropped by enemies to reinforce his reserves. In addition to his normal gun, any Bombs Hal collected outside the fortress (or within through the occasionally-dropped Bomb powerup) can be employed inside the fortress to create powerful explosive shots. Hal must navigate the increasingly complex and maze-like conditions of each fortress in an effort to locate the energy cores. To do this, he must ride elevators and use transport tubes. Some of the transport tubes are one-way trips, while others do not return Hal to the location he first came from. The interiors of the fortresses are occupied with a variety of enemies which Hal must attempt to safely clear in order to reduce the amount of damage he takes. Once the core is found shoot at it with your regular gun, or preferably bombs, to destroy it. After the core is destroyed, the fortress will go dark and begin to self-destruct. You will then have about three minutes to locate the Lightspeeder positioned somewhere in the fortress and escape before the fortress explodes. There is no visible countdown clock, but you can get a general feel for the time remaining by observing the screen. After about one minute, the fortress will rumble and begin to shake. When the lights start blinking in and out, move quickly because you now only have about one minute to go. After you successfully escape from the fortress, you will move on to the next fortress.
Even if you run out of Lightspeeders outside a fortress, run out of energy inside, or fail to escape before the fortress explodes, you will be able to continue, either right at that moment, or later on by recording the password provided to you when you die.
After clearing all eight fortresses, it turns out that there is a second quest to try. The second quest is naturally more difficult than the first. In terms of the fortress interiors, the first four fortresses of the second quest are identical to the first four of the first quest. The second four, stages 5 through 8, are structurally identical to their previous versions. However, the transport tubes found in these fortresses send you to different locations, requiring entirely different solutions the second time around.