Alien Missions
UFOs are sent out periodically to conduct a number of types of Alien Missions, some of whom the purpose is fairly inscrutable, others are fairly obvious in their reasoning. Especially once the Hyper-Wave Decoder is deployed knowing the mission of the aliens can help make strategic plans for further actions that the aliens may attempt in the near future.
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.
Aliens do not directly score for this mission.
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.
If successful the aliens will score 30 points, which is eventually subtracted from your score.
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.
If successful the aliens will score 50 points, which is eventually subtracted from your score.
Alien Infiltration
This Alien mission represents the worst threat to X-COM. 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.
If a government agrees to a pact then its funding will cease. If successful the aliens will score 150 points, which is eventually subtracted from your score.
Five UFOs take part in an Infiltration mission, landing in both the target and neighboring countries. Two of these are often Battleships. It has not been conclusively shown that shooting down the Battleships or assaulting the landed ships will stop the infiltration from succeeding. See the talk page for discussion on this matter.
When a country is successfully infiltrated an alien base will be created in or near the country. Always check for alien bases after infiltration missions. This way you can get points by destroying it and know how much money you will lose at the end of the month.
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.
If successful the aliens will score 50 points, and an extra 5 points per day which is eventually subtracted from your score.
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 fifty Geoscape Tokens (bases, waypoints, ships, etc) that can exist on the globe at any given time, and because you have to share this space with pretty much everything that you can interact with on the Geoscape, you can only have as many Alien bases as there are unused slots.
Note: UFO flight pattern investigation has found that the base is placed as soon as the battleship arrives in the atmosphere, so if it shows, the aliens have a base.
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.
If successful the aliens will score 1000 points, which is eventually subtracted from your score.
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.
Aliens do not directly score for this mission. Losing a base will give you negative points depending on what was in the base.
Alien Supply
Once an Alien base is constructed, it is resupplied on a regular basis by special supply vessels. If one of these vessels is detected while landing then it is certain that an Alien base is nearby.
Aliens do not directly score for this mission.
Note that supply ships on supply missions are always at a speed that makes them impossible to shoot down by interceptors, even shortly before landing or after taking off. This means they can only be attacked while landed unless new aircrafts have been researched and built. Since they will certainly land this would be a waste of Elerium since your craft will need some for the interception and the Elerium in the ship might be destroyed.
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!