53:1
The Eden Dispute
Farpoint receives a distress message from Giselle and Odette, now grown Dukhang females, who claim to be running a colony under attack by pirates. Hunter travels to Eden and finds a well-defended colony under attach by the Lucian Alliances. The Lucians board Hunter, almost crashing it into the atmosphere in order to bring down the colony's shields before retreating.
On the surface, a landing party finds a seemingly serene colony, which is soon attacked by Lucian ground forces. The team take shelter in hidden tunnels, which prove to be a hidden Dukhang birthing facility, complete with a device that is pacifying the colonists. The Goa'uld Polltrok, now working for the Lucian Alliance, teams up with Giselle and Odette, who want Corry Vrecken to mother a new race of Dukhang. Rogue Squadron's troops arrive in time to destroy the facility, but Giselle, Odette and Polltrok escape.
53:5
The Lost Empire
While investigating strange readings from a newly charted planet, around 100 crew from Hunter are teleported to an abandoned, overgrown city where they are unable to contact the ship. They are immediately attacked by a tribe of Jaffa who have seemingly being on the planet for many years, before being rescued by a band of stranded Imperials led by Captain Renshaw.
The Rogues navigate an ancient crash site and make their way across the city to the Core, a monolithic structure that Renshaw suspected was responsible from bringing them and numerous other unlucky crews to the surface. On reaching the Core, the group encounter vicious feral creatures but are able to shut down the device that was cloaking the city and kidnapping passing starship crews.
Returning to explore the crash site, they discover the remains of an ark ship that had presumably housed the last remnants of the lost civilisation, before being ambushed by Renshaw's Imperials until help arrives from Hunter.
53:9
Salvage Rights
Rogue Squadron liberates a cache of stolen alien artefacts from a downed Star Destroyer. On returning to Farpoint, they discover that one of the artefacts has an adverse reaction with the planet, causing disastrous earthquakes. After identifying the source the Ancient caverns below the planet, they quickly ship the artefacts off-world.
53:10
Exit Wound
Undercover, Rogue Squadron attempts to return an artefact stolen by the Star Destroyer Recluse to the planet Plek. Upon arrival, their men are singled out for participation in the capital city's gladiatorial games, until rescued by the remaining party.
By this time, the Rogues have been identified by remaining crew members from the Recluse, who are serving amongst the priesthood. Striking a bargain to complete their mission and help the Imperials escape, the plan falls apart again when they are exposed as off-worlders to the local leader.
After being thrown to a dragon-like creature, the Rogues identify a hidden Stargate and transport rings in the arena and are able to return to Hunter.
54:2
Innocence Lost
After responded to a distress call from Ketbrae, Rogue Squadron is stunned to discover the Lucian Alliance working with the Dukhang twins Giselle and Odette. They pursue them to Shedyet, where they find the Warrens—home to Shedyet's remaining population—abandoned and boobytrapped.
Finding inhabitants sheltering in a makeshift city, they make a last stand against the Lucians, but are taken as captives with others from the city. Amidst a space battle between Hunter and the Lucian ship, they are able to escape back to the Star Destroyer. In a ransacked TAG Lab, they find the Lucian agent Polltrok trying to find a weapon to destroy the twins.
The twins capture Corry Vrecken and Nick Fel and attempt to escape the ship, torturing Nick in the process. When their ship proves to be disabled, they attempt instead to capture Hunter. In a stand-off on the bridge, a vial of Dukhang poison developed by Corry is unleashed, killing the twins.
Afterwards, the Warren's population is re-homed on Farpoint, which opens its doors to refugee. Mike Burn reveals to Nick that the twins survived and are being held in a comatose state beneath the base.
54:6
Enemy at the Gates
Amidst high tensions between Farpoint and the new city around it, unknown enemies sneak in with refugees and incite a riot, in which many Rogue Squadron personnel are caught up.
As the intruders use the chaos to gain access to the base, those trapped outside the city pursue them to a cloaked camp in the nearby mountains, with the help of the city's leader and militia.
Although none of the infiltrators survive, their equipment suggests they belong to the shadowier elements of New Republic Intelligence.