Rogue Squadron's history is broken up into the following story arcs:
The Goa'uld threat is discovered in the Unknown Regions, and a new task force is quickly assembled to deal with it.
The Move to Farpoint
The task force moves to a new permanent home on the planet Farpoint.
The Fall of Sobek
Action is taken as the Steele-Sobek alliance's ultimate weapon nears completion.
Eye of the Storm
In a period of relative peace, Rogue Squadron skirmishes with smaller Goa'uld intrusions.
Pirates of Wild Space
Pirate groups operating on the fringes of Known Space begin to encroach on Rogue Squadron's operations.
Dissident New Republic Intelligence agents cause grief for members of Rogue Squadron.
The Holy Grail
Rogue Squadron races across Goa'uld space to reclaim an Ancient artefact.
A New Threat
A mysterious Goa'uld reorganises formerly allied forces against Rogue Squadron.
The Fight Back
Rogue Squadron launches a series of attempts to set back the new Goa'uld leader's efforts.
Rogue Squadron comes up against the System Lord Ba'al and his new associate--the cloned Imperial General Malphuus.
Khepri the Betrayer
Rogue Squadron forms a shakey alliance with a devious System Lord.
The New Empire
Malphuus begins a quest for advanced technology, leading Rogue Squadron to seek new allies.
Rogue Squadron is caught in a war between Malphuus's empire and a break-away faction.
Betrayal brings Rogue Squadron to the brink of tearing itself apart.
The Dukhang Crisis
Rogue Squadron battles a fearsome new enemy.
As Rogue Squadron learns the true origins of the Dukhang, a means to end their rampage is uncovered.
As planets across the Unknown Regions recover from the Dukhang Crisis, an old enemy attempts to solidify their power.
After the War
The Triumvirate and Imperial Union have been defeated and their leaders presumed dead. But peace is not so easy to find.