Secondary Objectives are random events that alter the flow of the mission by providing tasks that players must accomplish before they can proceed with the mission.
Sometimes enemies will activate "lockdown." This closes most doors, and players have to hack a control console to open them back up. However, this does not lock elevators. Depending on the situation, a lockdown can actually be beneficial for the player by locking out additional enemies and locking in of him/herself with a fixed number of enemies in the room, or put the player in serious trouble by the locking in of him/herself with said fixed number of enemies.
Lockdown happens most commonly if the alarm has been triggered and players neglect from from resetting it, or at the beginning of a mission experiencing a Battle Damage/Self-Destruct environmental hazard.
Lockdown can also be caused by breaking Reinforced Glass during missions that take place in spaceships.
Note that enemies have to run to a control console themselves to activate lockdown. Killing them before they reach the console can prevent a lockdown. There seems to be a minimum delay between different enemies attempting to trigger a lockdown but the exact time has yet to be determined.
The implementation of new animations for enemy interaction with consoles created a significant delay between the time an enemy places a hand on the console and the actual triggering of the lockdown. During this time the interacting enemy can be killed to cancel the lockdown. An enemy may also glitch and run rapidly around the console (clipping through terrain in the process) while attempting to initiate the animations, although whether this prevents other enemies from using the console is unknown. It also seems when an interacting enemy is suddenly been knocked out of the console but not killed or been removed by Mag's Pull ability, a lockdown will immediately set off.
Certain mission types can trigger a timed extraction upon completion. When you reach your goal, a timer will activate. If players do not reach the extraction point before the timer runs out, they will fail the mission. This is most problematic if an additional objective is triggered, especially a rescue mission.
Sometimes when players complete their primary objective, they will be informed that there is a second primary objective. This can be any of the main objectives, even duplicated ones. This objective is usually predetermined at the start of the mission as you can explore the area of the second primary objective ahead of it being set as the current primary objective.
For instance, the players have destroyed the reactor core, but instead of being given the extraction location, they are given the location of a hostage, and are required to rescue them before they can be extracted. This can coincide with the timed extraction event, making for a hectic run.
Secondary Objectives can also take effect even before the original objective has been completed, in which case the new objective will replace the original objective as the primary mission. For example, players in a Sabotage mission may be informed that there's been a change of plans, and that they now need to kill all enemies, turning the mission into an Extermination. Objects pertaining to the original objective, like Reactors and Capture Targets will still be available, but will become unimportant in finishing the mission unless the new mission objective requires said objects.
Although Raid missions were replaced by survival, it's possible to get a raid mission as an additional objective as of Update 10.0.