The Mega Fortress Experimental Mobile Factory (unlocked via the "Air Fortress" research) is a UEF major experimental unit. It is an air-based Air Factory, capable of manufacturing any non-experimental air unit (including transports) at a faster rate and much lower cost than a UEF Air Factory; and storing up to 25 units in its hold. It is equipped with 4 anti-air weapons as well as 8 anti-ground weapons, making it effective against every type except submerged units. It's biggest damage is when it falls out of the sky and crushes what it lands on.
While the Mega Fortress couldn't defeat most air threats if it's life depended on it (which, in most cases, it does), it boasts more than impressive anti-land weapons. It easily out damages an AC-1000, and can destroy a Fatboy II in a matter of seconds.
The Mega Fortress is much more costly than an AC-1000, and hence less cost effective. It is also less mobile (unless flying in a straight line). While the Mega Fortress should not be used for assault purposes, it makes for excellent base defense.
The Mega Fortress can produce all basic air units (however, it cannot store the C18 Star Lifter Air Transport). Using the Mega Fortress is a cost-effective method of producing air units as it uses only 1/3rd of the resources and takes 1/3rd the time of the standard Air Factory. This means that for the same price, and in the same amount of time, the Mega Fortress will produce three times more units than a standard factory. It can also be assisted by engineers and the ACU just like a standard Air Factory. on maps like Geothermal Borehole with limited space they can be effective space savers.
To deploy the units on PC, use the toolbar and select "Unload", much like a C18 Star Lifter or Commander-Class Aircraft Carrier.
To unload the units on Xbox 360 hold the left trigger and press left on the d-pad. Then select where you want the units to travel.
Do not send it alone into battle, as its anti-air defense are terrible at landing hits on fighters. Ideally, avoid using it offensively at all. It is worth far more as a factory then as a gunship. If going up against illuminate air with flares, the anti-air is completely useless, as the flares will recharge after 2 salvos.
Its best use is as a replacement for your air factories, as it builds units much cheaper and quicker and can move to avoid being the target of nukes.
A good strategy is to park it right outside the enemy's range of AA defenses, and have a repeat build order and occasionally deploy all garrisoned units.
As with all mobile construction units, it will not deploy constructed units until it receives an explicit unload order. Clicking right next to it will cause all units to exit immediately.
It is a good idea to have an engineer assist the air fortress to increase its build speed further, and heal it if it becomes damaged. Two engineers for purposes of build speed is likely overkill, while three certainly is.
Without engineers assisting or increased energy through research, the air fortress takes a little less than 6 energy generators (with mass convertion) to sustain constant construction.
You can also use the Air Fortress as a node in a longer unit deployment chain. If you want to deploy units outside the Noah Unit Cannon's range, you can park the Air Fortress near where your land units land from the Cannon, then have C18 Star Lifters ferry them the rest of the way while using the Air Fortress to produce air escorts and additional transports if they get shot down. This can also effectively prevent your opponent from destroying the land units as they hit the ground, which is a common problem when using the Noah.
Mid to late game it is possible to have several air fortresses creating a 'disposable' air force that can be sent against a superior army wave after wave, due to UEF bombers and fighters being cheap/fast to build initially, and now 3x as much with the air fortress.
During the campaign, if you've built a mega fortress, it is wise to build Wasps right away, since it will be targeted right away by enemy fighters.
After building 18 wasps, it becomes cheaper than having an air factory
The Mega Fortresses can also benefit from being the quickest Major Experimental to research.
To obliterate most of a base, build about 20, have each of them build 5 Wasps, and then group them. Move right outside of their base (out of range of AA) and then send the fighters in. While the AA towers and other fighters are distracted, send in the Mega Fortresses (AC 1000s help as well, about 5) to kill the commander. Even if they get taken out, the air crashes will get most of the base, making it easy pickings for some Nuclear Warheads.
This unit may not be able to take out sumbarins or the Atlantis 2, but the air craft it has stored in its hull can...
BUG: (on the 360) If you have a Mega Fortress spam the stop button. You will be able to freeze the game when it gets destroyed. This isn't recommended, as it will force you to turn your Xbox 360 off and then on again.