Retroactive Continuity, commonly referred to as a retcon, is the act of altering established cannon of a fictional work. These changes are usually done in order to deal with continuity errors, or to work new material into an established fiction with which it might not properly mesh.
The "City Of" franchise has seen numerous small alterations of this nature, and several large ones, during its years. In most cases, these changes are to the rank of an NPC (such as Frostfire, who used to be just a boss, and now is an Elite Boss), where something is located (creating new zones that have always been there), and even an occasional correction to an NPC's gender or genetic origin.
Following is a list of some of the known retcons to the game's continuity. It is not a complete list, but contains some of the larger retcons.
With Issue 3, the 5th Column, one of the most popular factions of the game, was replaced with a new, more modern, enemy group, the Council. In this replacement, all previous stories, arcs, badges, and any references to them in-game were outright replaced to be about the new group. Reasons for this change are still unknown and widely debated (See 5th Column Controversy), but regardless of why, this was the single largest rewrite of the game's history so far performed.
Originally, when Striga Isle was added to City of Heroes in Issue 3, there were many references to a splinter faction of the Council called "Spider" that The Center detested. Later on at some point during the creation of City of Villains, the faction was changed to Arachnos.