Alien Infiltration (Apocalypse)
Alien Infiltration occurs when the aliens directly deploy alien life forms into buildings. Aliens will then spread through the organization that owns the building and other buildings next to the original one (and infiltrating other organizations). If left unchecked it will progress as time goes by. When infiltration crosses a threshold (above 50%) the organization may revert to alien control and will turn hostile to X-COM.
This alien tactic can be stopped by conducting early searches on buildings of the affected organizations, especially the original building point of infiltration. In It is possible to see the UFO deploying the aliens on City Display when using the Isometric View (it hovers above a building and uses a grey tube).
Alien Subversion
Subversion can turn immediately the organization to the aliens's side, depending on luck. It will done by UFOs hovering above a building and dropping a blue 'rain' over its target (again visible with Isometric). The only way for X-COM to stop this method is to shoot down any UFOs before they are able to finish their actions over the buildings. Since the location of the Dimension Gates is regularly changed this can result in gaps on X-COM aerial coverage of the city. By destroying the alien fleet of UFOs X-COM can prevent any further infiltration/subversion to occur on the city.