The Atlantis II Experimental Aircraft Carrier is a UEF minor experimental unit designed to produce air units, engage submarines, and even bombard shore targets with battleship-class weaponry. However it does not have anti-air capabilities. Too big to be created from a Naval Gantry, the Atlantis, like it's cybran counterpart, has to be built, as a 'structure' by an engineer or the ACU in open waters.
Contrary to popular belief, the Atlantis II is a very powerful unit, not just a "submersible movable factory". For almost the same price as the Poseidon, the Atlantis has more health, more weaponry, and is more combat capable than the Battleship. In direct combat with a Battleship, the Atlantis II will win easily. It is also equipped with relatively powerful torpedo weaponry, making it even more effective at naval combat.
However It lacks anti-air weaponry, but it can be easily protected by the Wasps it creates itself or by simply submerging (unless you're up against torpedo bombing Eagle Eyes). The fact that it can submerge makes it a very deadly assassin-type unit (it can destroy targets of opportunity, like naval factories). Its large size easily backs up its menacing looks, though this comes at the cost of sluggish movement speed.
The Atlantis II has a very low range (50, compared to the Poseidon's 128). As such, the Atlantis II is only useful in direct combat and cannot be used to shell land targets. If you need to bombard land or destroy units from a distance, use Battleships. Since the Atlantis II is submersible, it can come to close range to a target submerged and rise to destroy it. The Atlantis II can be used like the Kraken.
A powerful formation is to have a few Atlantii in your front lines, tanking for a bigger line of Battleships in the rear line. This way, the Battleships can safely destroy anything from a distance while the Atlantii II take care of any direct naval threat. The Atlantis II should protect the battleships, and not the other way around. You can also mix in some Tigershark Submarines for added effectiveness. If you are attacked by other Battleships, have the Atlantis II submerge to intercept the Battleships.
The Atlantis II can produce almost all basic air units (except for the C18 Star Lifter Air Transport). It will build these units at exactly 1/3rd the cost of the Air Factory, and at exactly the same speed.
Only torpedoes and the Illuminate Wilfinja can attack a Submerged Atlantis II. Use this to extend its life.
The Atlantis II can build units while submerged, though start atomaticaly deploying onc its storage of 25 units is full.
Being able to submerge, an Atlantis II can swim up beside an sea-side enemy base, surface, and launch a full complement of 25 bombers before submerging to build 25 more units, resurface and repeat, maintaining its assault.
Use them to trick your opponents' war effort into anti-air and attack with a land force. (destoying a few battleship patrols with air will suffice)
It's torpedoes make it devastating against enemy navy especially if submerged and the enemy has no counters to submerged units (other Atlantii, Illuminate Wilfindja, blobs of Tigersharks, and Eagle Eye torpedo bombers.). Do not surface if severely outnumbered, though an Atlantis will easily destroy a battleship, more than 2-3 at a time is likely suicide.
The Atlantis' short range makes it very vulnerable to kiting, particularly by Poseidon Battleships and Executioner Battleships. Use this to your advantage. Do note however, the Atlantis can easily build aircraft to make up for this, particularly torpedo-tube-equipped Eagle Eyes. Also if the Atlantis gets too close, you're screwed all over.
It has traded its anti-air guns for direct-fire weaponry, and has a reduced capacity (25 compared to the 150 of its predecessor). The Atlantis II is significantly less notorious than its predecessor and less used on water maps than the common battleship while in SC1 and Forged Alliance a battleship was very rare.