Queenspawn (Apocalypse)
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There's only one in the game, found in the spawning chamber alien building. Capturing this alien alive gives you Alien Gas weapons, though by the time you're here your victory is probably assured anyway. The queen has a powerful spit attack and apparently has VERY POWERFUL claws on its appendages, but she's immobile so both of these are easily avoided. This means you can safely clear out the rest of the map and leave her to the end.
To Capture: In order to capture it alive clear out the rest of the map and take out the reinforcement teleporters and have your men stand back and serially throw stun grenades at the Queenspawn. You may need to run in and out to avoid taking too much damage from her spit, but with the teleporters gone time is on your side. Once it's well and truly gassed up, shoot it a bit with a light weapon and you're done.
Official Entry (Captured Alive): "The Alien queen is ultimately the production unit for all Alien life forms. Its mobility is severely limited when fully grown and it also requires exactly the right atmospheric conditions in order to breed properly and produce the Alien eggs. These conditions are only provided by the spawning chambers inside an Alien building, which also provide a food source by plugging directly into the Queenspawn's blood supply. This confirms that the Aliens cannot conquer our dimension without a steady supply of Alien reinforcements through the Dimension Gates, although their motive for such incursions is still unknown."
Official Entry (Autopsy): "The massive form of the Alien queen is designed to lay huge numbers of Alien eggs during its life time. The Queenspawn uses a complex asexual reproduction system to produce large numbers of Alien eggs in order to create new types of Alien creature. The importance of the Queenspawn for Alien population growth makes it an important strategic target."