Rogue Squadron's history is broken up into the following story arcs:
45:1
Foundation
The Goa'uld threat is discovered in the Unknown Regions, and a new task force is quickly assembled to deal with it.
46:5
The Move to Farpoint
The task force moves to a new permanent home on the planet Farpoint.
47:5
The Fall of Sobek
Action is taken as the Steele-Sobek alliance's ultimate weapon nears completion.
48:1
Eye of the Storm
In a period of relative peace, Rogue Squadron skirmishes with smaller Goa'uld intrusions.
48:2
Pirates of Wild Space
Pirate groups operating on the fringes of Known Space begin to encroach on Rogue Squadron's operations.
48:4
Internal Strife
Dissident New Republic Intelligence agents cause grief for members of Rogue Squadron.
48:5
The Holy Grail
Rogue Squadron races across Goa'uld space to reclaim an Ancient artefact.
48:5
A New Threat
A mysterious Goa'uld reorganises formerly allied forces against Rogue Squadron.
48:6
The Fight Back
Rogue Squadron launches a series of attempts to set back the new Goa'uld leader's efforts.
49:1
Malphuus Resurfaces
Rogue Squadron comes up against the System Lord Ba'al and his new associate--the cloned Imperial General Malphuus.
49:4
Khepri the Betrayer
Rogue Squadron forms a shakey alliance with a devious System Lord.
49:7
The New Empire
Malphuus begins a quest for advanced technology, leading Rogue Squadron to seek new allies.
49:10
The Triumvirate
Rogue Squadron is caught in a war between Malphuus's empire and a break-away faction.
50:3
Dissension
Betrayal brings Rogue Squadron to the brink of tearing itself apart.
50:6
The Dukhang Crisis
Rogue Squadron battles a fearsome new enemy.
51:1
Nefru's Fury
As Rogue Squadron learns the true origins of the Dukhang, a means to end their rampage is uncovered.
51:7
Triumvirate Resurgent
As planets across the Unknown Regions recover from the Dukhang Crisis, an old enemy attempts to solidify their power.
53:1
After the War
The Triumvirate and Imperial Union have been defeated and their leaders presumed dead. But peace is not so easy to find.