The Second Systems Commonwealth Civil War was a series of events orchestrated by the Spirit of the Abyss to try and destroy the New Systems Commonwealth, in order to splinter all organized resistance that might oppose the Magog World Ship as it rampaged through the known galaxies. The Abyss almost succeeded in destroying the New Commonwealth.
Agents from the Special Collections Division of the renowned All Systems University had for years been hunted by the Spirit of the Abyss and its followers. However, as the New Systems Commonwealth began to form, in response many of those followers consolidated their positions and infiltrated the Collectors organization that was part of the New Commonwealth. Eventually, they managed to form a separate but powerful faction within the Collectors, eventually taking over the Collectors, and using their knowledge to subvert the Commonwealth government for their own personal needs, and to aid the Abyss. These Collectors played an extremely influential role in the Second Civil War, and actually obstructed supply lines and the arrival of ships to the battlefield. They even tried to lure surviving Commonwealth vessels from the Battle of Enga's Redoubt to a planet so that they could be decimated. However, the rogue Collector faction was slowly decimated as the Commonwealth Civil War continued.
Right from the start of the revived Commonwealth, the Nietzscheans disapproved of it. Many prides did eventually sign the charter, but only because of the defensive options, and political and economic backing that being a member of the Commonwealth afforded. However, they believed that it was even weaker than the original Systems Commonwealth, and often openly defied the Commonwealth's wishes. Some of the more powerful prides ignored and often even fought the Commonwealth. By the opening Battle of Enga's Redoubt, the Nietzscheans had been planning and making secret alliances for some time, ones that would try and unite all the prides together so that they could finally form a Nietzschean Empire.
The Andromeda Ascendant was informed by Minister of War Jane Rollins that the Nietzscheans have been attacking independent worlds, and have been seen massing their fleet around the Drago homeworld of Enga's Redoubt. She is also informed that the Nietzscheans are ceding en masse from the new Commonwealth. The Andromeda was then ordered to go to Enga's Redoubt to assess the situation, and to open negotiations if possible. When the ship exited slipstream in orbit of the planet, she was immediately cripples by sabotage by Tyr Anasazi. Nietzscheans boarded the vessel to try and take back Drago Musevini's bones, but they failed. The Andromeda then had to stay helpless in orbit and watch the New Commonwealth fleet get decimated at the Battle of Enga's Redoubt.
Once again, 3 years after the reformation of the Systems Commonwealth, the Nietzscheans betrayed the Commonwealth. However, unlike the first insurrection, they had the support of the Collectors and the Spirit of the Abyss. This time, Tyr Anasazi, a member of Captain Dylan Hunt's own crew, had been forming plans to take control of the Nietzschean people and reunite them. He spent years sabotaging the Andromeda Ascendant's systems, so that at a crucial moment the Andromeda could be kept out of commission, therefore posing no danger to his plans. He had his DNA replaced with that of Tamerlane Anasazi, who is the Nietzschean Messiah, the genetic reincarnation of Drago Museveni. He used his newfound Messianic power, and assumed control of the Nietzscheans. All of the Commonwealth's enemies also had joined together and destroyed both the Drago-Kazov Pride and the High Guard fleet at the Battle of Enga's Redoubt. The Secession took a heavy toll on the Restored Commonwealth: at least 1 entire system was destroyed, the Perseid planet Xinti was occupied, and many of the new High Guard's prized vessels were also destroyed. And once again, a power vacuum brought to light the true powers behind the Commonwealth. Later, it is also discovered that the Nietzscheans were working with the Spirit of the Abyss.
The Battle of ArkologyEdit
See: Battle of Arkology
The Andromeda fought against the Magog World Ship in a final attempt to save the galaxies from the enroaching Magog fleet. The entire crew, and the ship, were believed to have been destroyed, though in fact they had journeyed through the Route of Ages to avoid destruction and to survive the battle.