Alien Missions
Alien Research
The Alien research mission is used for collecting basic data on Earth and its inhabitants. Small vehicles are predominantly used, with occasional landings in deserted areas. This type of Alien activity poses the least threat to X-COM, with little concern from governments or the public.
Alien Harvest
The Aliens have many uses for Earth's fauna. Animals are abducted secretly, and returned with various organs removed. Cattle mutilations are predominantly reported along with UFO sightings. This type of Alien activity causes great concern by governments and considerable anxiety amongst the population. This type of activity occurs mainly in farming land. The theory behind the 'Alien Harvest' suggests that Alien races originally "seeded" the planet with its flora and fauna, and now they have returned to reap the harvest they have sown.
Alien Abduction
This is the most insidious form of Alien activity. The abduction by Aliens is widely reported, despite the Aliens' attempts to erase the experience from their victims' memories. Abductees report being subject to humiliating physical examinations, including impregnation of alien foetuses and bizarre genetic experiments. The purpose behind this activity appears to be linked to genetic mutation and manipulation of the Aliens own genetic material. This activity causes great alarm, and occurs in populated areas or cities.
Alien Infiltration
Earth governments can be infiltrated by Alien agents which are Human in appearance. This can result in official contact between Aliens and governments at the highest level. The climax of this activity is characterised by intense UFO activity in the vicinity of major cities. The aliens will attempt to sign a pact with an earth government by offering knowledge of their superior technology. In return, the government will allow the Aliens to conduct their activity unhindered. This Alien mission represents the worst threat to X-COM. If a government agrees to a pact then its funding will cease.
Additional Information
Five UFOs take part in an Infiltration mission, landing in both the target and neighboring countries. Two of these are often Battleships. There is limited conclusive evidence to say whether shooting down the Battleships or simply assaulting a landed ship will stop the infiltration from succeeding. Results will vary greatly no matter the outcome.
Zombie says, "According to my preliminary results, Russia cannot be infiltrated in the CE version of X-COM so losing the game by this method is impossible." (Jun 16, 2005, StrategyCore forums)
Several players have however offered a different opinion on this matter and have lost Russia.
Alien Base
Aliens will construct secret underground bases in remote locations. After some initial reconnaissance flights some intense UFO activity will occur as the base is being built. These bases are known to contain experimental labs for human abductees, and supplies for further activity in the region. The presence of Alien bases will generate a large amount of reported Alien activity without the presence of UFOs. In order to locate a base, an X-COM craft must patrol an area for a few hours to stand some chance of detection. An Alien Base Assault will remove the threat but should never be taken lightly.
Additional Information
There is no limit to the number of alien bases that can be built, but there is a limit as to how many can exist on the globe at the same time.
Only a limited number of Geoscape Tokens (bases, waypoints, ships, etc) that can exist on the globe at any given time: 50.
Because you have to share this space with pretty much everything that you can interact with on the Geoscape, you can have as many Alien bases as there are unused slots.
Alien Terror
When the Aliens terrorise a city, they will deploy some special forces with awesome powers. Civilians will be directly threatened, and governments will be forced to evacuate whole areas. The main purpose behind this activity is to generate sufficient public hysteria so that governments will threaten the X-COM project.
Alien Retaliation
If X-COM Interceptors are being particularly successful in shooting down UFOs then the Aliens may take some retaliatory action. This could result in a direct attack against an X-COM base. However, the aliens have to find an X-COM base in order to attack it, and provided UFOs are kept away then there should be little danger of an assault.
Additional Information
Sometimes the very first UFO you encounter in a brand new game will be a Retaliation Scout. Do not be alarmed if your base is attacked almost immediately. This is normal. You don't have to like it, though.
Shooting down the retaliation scouts may prevent a base assault, but shooting them down close to your base almost guarantees an attack. Therefore, shoot down retaliation scouts with great care.
Retaliation missions consist of the scout that loks for your base. When found, it is followed up by a Battleship dropship carrying a team of aliens that are to be inserted into your base. The assault team consists of aliens that you can find manning Battleships and Alien Bases. The Battleship vanishes once it has inserted the troops - presumably escaping into the atmosphere during the attack.
Each retaliation wave consists of a single group of aliens that are seeking to destroy your base. Each group, which can be of the same species, will independantly target your base for retaliation. Once your base is located, they will continuously send Battleships at the base until one breaks through your defences. They will not stop until this happens.
Once they manage to drop a retaliation squad into your base the group sending the battleships will have a sudden case of amnesia and forget the base location. Why this is a bit of mystery, but what's important is that you will not have to worry about another attack until the retaliation scouts appear.
If you are being targeted by several groups of aliens at the same time, you will have to crush both (or all) of the assault squads before the aliens stop attacking your base.
A few quick conclusions: First, each wave of retaliation ends when the retaliation squad is inserted into the base - then the base is forgotten. Second, an impenetrable base is highly discouraged as it will never be left alone until the battleships are let through.
Alien Supply
Once an Alien base is constructed, then it is resupplied on a regular basis by a special supply vessel. If one of these vessels is detected while landing then it is certain that an Alien base is nearby.
Piracy time. You may want to let the Alien base exist, just for millions of dollars plundered from the Supply "Blimps". Arrrrrr, avast ye Space-Lubbers!
Cydonia
This special, final mission has its own page here.