There are some script commands that you can (theoretically) use to change the atmosphere.

The triggering event:
Code
OnTimer (FIXEDSTRING:timerName)
Throw when a timer has ended


Funcs that change the atmosphere:
Code
SetAtmosphere (FIXEDSTRING atmosphereTriggerUUID, FIXEDSTRING atmosphere)
Changes the atmosphere of the trigger

ResetAtmosphere (FIXEDSTRING atmosphereTriggerUUID)
Resets the atmosphere of the trigger