Mega-Primus
The city is run by 13 elected senators. Large corporations maintain the environmental, social and economic structure of the city, while the populace live in relative comfort. Mega-Primus has its own marginalized minorities, consisting of Sectoid-human hybrids and androids, both by-products of the previous wars. These minorities have set up their own political pressure groups. When the aliens invade, the city government reestablishes X-COM. This time there is no absolute support by world/city governments. Mega-Primus has its own governing body who supply nearly all of X-COM's income. X-COM would have to support its income through the sale of alien artifacts captured from missions, and items manufactured in their own workshops.
X-COM must maintain a good rapport with other organizations in the city. If X-COM angers any of them, or fails to contain the alien incursion, organizations will demand compensation or even actively attack X-COM forces. They will also withdraw their support (if any) for the X-COM project. For example, the Transtellar organization would prevent Agents and science personnel from travelling around the city. The corporations and political organizations will make profits, perform research, manufacture items, and even fight covert battles with one another independently of the player. For example, if Megapol, the city police, are making lots of money, they will be able to maintain a strong presence in the city, attacking alien ships and other hostile aircraft. The more damage to the city, and the greater Megapol's financial trouble, the less they will be able to respond to enemy attacks across the city. One of these organizations, the Cult of Sirius, is a group of religious fanatics who worship the aliens, and is inherently hostile to X-COM. The aliens, rather than simply signing non-aggression treaties with the various corporations, will attempt to infest their CEOs and take control of the organizations themselves.
If the Government becomes hostile towards X-COM for any reason, such as alien interference or excessive damage to Government property and personnel, then the X-COM project will receive no further funding. This is a potential disaster for the player, and can lead to X-COM scrounging out a miserable existence, stealing from other organisations in order to survive. However, with perfect management, X-COM can outpower the entire City's military, while being richer than even Food Monopoly Company Nutrivend, then destroy the whole city and get away with it. Having friendly relations with both minorities (the android organisation S.E.L.F and the hybrid Mutant Alliance) can result in talented recruits of these races becoming available in following weeks.
Plot
Half a century after the end of the second X-COM campaign, the last battle of T'leth has severely damaged Earth's biosphere. As a result, several self-contained Megalopolis-type cities were proposed to provide habitation for humanity. The game follows Mega-Primus, the first of these cities, built over the ruins of Toronto, Canada. Meanwhile, the off-world colony of Mars is exploited by the Elerium mining corporation, Solmine, and oppressed by MarSec (MARs SECurity).
The alien threat in the game is presented by a new race of organic, extradimensional aliens that initially seem to have no relation to the aliens of the previous two games, though later missions set in the aliens' home dimension reveal they have enslaved Sectoid survivors. These new aliens attack the city through tetrahedron-shaped teleport gates. The player must find out how to send their own aircraft, along with X-COM agents, through these gates without being destroyed and take the war to the aliens. Apocalypse has 14 races of alien beings including Anthropods, Brainsuckers, Hyperworms, Megaspawns, and Micronoids. Each race has various strengths and weaknesses, and some races are dependent on other races. The "alien life cycle" plays a crucial role in the game.
The player is exposed to this "alien life cycle" through research and more importantly the lower level alien attacks during specimen gathering combat. Primarily the attack of the weaponized alien the Brain-Sucker which attacks individuals after landing from a pod launcher utilized by alien foot soldiers. The Brain-Sucker hatches and attacks the nearest individual by jumping on their head and seemingly injecting something into them through the mouth and dying immediately after the attempt.
The life cycle later takes a mysterious turn as it shows no connection between the lower alien forms and higher alien forms. Eventually, however, it is found that the leaders of the invasion are the Micronoids, a race of sapient, single-celled organisms that live in the bloodstreams of the other aliens. The ultimate goal of the invasion is to inject Micronoids into the bloodstreams of important figures, allowing them to control Mega-Primus through psionic domination of their hosts. The player is eventually tasked with invading the aliens' homeworld and destroying their side of the gate to stop the Micronoid infestation.