Cityscape Fighting (Apocalypse)
These are the types of missions that can occur on Mega-Primus.
Infiltration/Subversion
The UFO's will hover over buildings and will either directly infiltrate aliens into the building (through a transport beam visible on the Cityscape Screen) or try to directly subvert the organization (through the 'Micronoid Rain' attack which is also possible to see with Overhead View). If an X-COM Base is present at the building a Base Defense Battlescape mission will immediately take place.
Usually those missions will also involve fighting between the UFOs and Megapol's police cars, even if X-COM doesn't launch any craft to stop the alien craft.
Retaliation
Aliens
The aliens will target an organization and will conduct attacks with their craft with the propose of destroying the organization's buildings and craft. If the target is an X-COM Base then the entire structure can collapse (especially in the case of Slums). If the map square with the Agent figure is destroyed it will bring the death of any X-COM personnel allocated to that base.
Overspawn Drop
Same as before but instead of using the massive firepower of their larger craft the aliens will drop an Overspawn into Mega-Primus with the same objective of conducting massive damage to the city (and the corresponding negative impact on X-COM's score).
X-COM
Another possibility is for X-COM to engage on bombing raids of its own because of the negative score points earned by damage inflicted by X-COM craft to the city with no other result than emotional satisfaction (and the targeted organization demanding more money afterwards).
This also forces the victim to spend money rebuilding their structures, and can help bankrupt them or otherwise put a serious dent in their wallets.
Other Organizations
Less frequently an organization might instead send illegal flyers to directly attack the buildings of their enemies. Sometimes it might be a good idea for X-COM craft to intercept and destroy illegal craft heading towards its allies or merely to prevent more damage inflicted to the city.
Raiding
Organizations hostile to one another will conduct economic raids which will be reported by messages on the Message Bar. X-COM can conduct raids of its own with the propose of recovering valuable items or as a means of punishment. If it is X-COM who finds itself targeted then a Base Defense mission will occur.