Biological Warfare (Apocalypse)
Biological Warfare can be considered the ultimate human-designed weapon to fight the aliens. Either this or the Devastator Cannon can be considered your "standard issue" alien-slaying weapon in the mid-to-late game.
The Toxigun is one of the most powerful weapons in the game, available upon the completion of Biological Warfare research. Not only do the toxins specifically target alien biologies, but Toxigun shots pass through Personal Disruptor Shields. This effectively increases toxigun damage against shielded enemies by a breathtaking amount, and allows the shields to be recovered intact as a side benefit. The only problem is that other agents without toxiguns will have to burn through the shield to help, so toxiguns don't combine very well with other weapons.
The Toxigun has a very high rate of fire, but is coupled with a small ammunition capacity and moderate accuracy. This means that agents armed with the Toxigun can empty the gun very quickly without doing much damage if they are not careful. To conserve ammunition, make careful use of the gun by using aimed shots (which are still quite rapid) or getting close to the target or using them in tandem with rechargeable weapons.
Because the toxin is designed to target aliens, the Toxigun will do damage comparable to the M4000 against human adversaries. The toxigun's ability to pierce shields means it is still a competitive weapon against shielded humans.
"An X-COM weapon designed to shoot high powered projectiles containing anti-Alien toxic fluids. It is designed to cause minimal harm to other targets and is not very good at penetrating armor."
Toxin A is available the moment the Toxigun is researched and is the weakest of the three toxins. This can be almost immediately replaced with Toxin B, as most of the prerequisites can be finished before the Advanced Lab is built.
"Ammunition for Toxigun. It contains a lethal fast acting poison designed to target Alien life forms. It is not so effective against the more advanced bipedal Alien types."
Toxin B offers an improvement of damage over Toxin A. It will be your primary toxin until the the final tier of UFOs and aliens show up.
"Ammunition for Toxigun. It contains a lethal fast acting poison designed to target Alien lifeforms. It effectively renders the earlier A-type toxin obsolete because it is more powerful and more effective against the higher Alien life forms."
Toxin C is the most powerful of the Toxigun ammunition, and is even more lethal than disruptor weapons.
The Real Alien Threat; Toxin Type B
"Ammunition for Toxigun. A fast acting poison which targets all Alien life forms with equally devastating effects. This toxin effectively supersedes the A or B types."