In the season finale, Andromeda encounters the Magog World ship, a structure of twenty connected planets and an artificial sun.
The World ship contains trillions of Magog and is equipped with a powerful weapon which creates miniature black holes.
Ethlie Ann Vare, another writer, rounds out the list of people who departed the show this season.
However, by the end of the season, the new Commonwealth had gained a new powerful war fleet and a total of fifty worlds.
For season three, Bob Engels was brought on the writing staff to fill the hole in that had been left by the departure of Robert Hewitt Wolfe and Ethlie Ann Vare.
The weight was mostly taken up by new writers: Larry and Paul Barber, who had no previous involvement with the show, wrote the bulk of season four.
Other newcomers included Ted Mann, Scott Frost, John Kirk, Lawrence Meyers, and the team of Lu Abbott and Stacey Berman-Woodward, none of whom contributed more than one episode.
The Collectors (originally keepers of historical information unknown to anyone else), allied with the Spirit of the Abyss, manipulate the fragile government of the New Commonwealth to show him in a bad light.
Trance asks Dylan to escape on a slip fighter through the Route of Ages, claiming that now there is nothing more important than saving his life; Marlowe, Arkology's leader (who had disappeared several hours before the battle) tells Dylan that they both are Paradine, two of the few ancient beings with incredible powers.
Dylan reluctantly leaves through the Route (in a strange sequence where he finds himself in a large dark room and seemingly meets another version of himself).
Trance partially recharges the ship's generators, but Andromeda still cannot move (apparently it needs 100 percent power) and its AI behavior is erratic.
The first half of the season deals with three main themes: Dylan's conflict with his crew, his attempts to restore Andromeda's power and the eventual discovery of the true role of Trance and the Seefra system.
Rhade, Beka and Harper are all angry at Dylan for leaving them behind in the Battle of Arkology and for throwing them to Seefra without any way to get back to the Known Worlds.
Their loyalty is strained several times, but seems finally reaffirmed after the intervention by Stranger, a Paradine sent by Dylan from an alternate future.
Andromeda's power is eventually restored with ancient Vedran artifacts, but it is still unable to leave Seefra, it seems to be located in a "pocket universe" and the only way out is the Route of Ages.
Seefra turns out to be Tarn-Vedra, the long-lost capital of the Commonwealth, but the Vedrans themselves left it long ago, disillusioned with humans.
Tarn-Vedra's original sun was somehow replaced by two artificial constructs, Methus-1 and Methus-2, but it's now damaged and emits deadly flares, which are the reason for Seefra's drought.
The Methus Diagram — a blueprint for the Seefra system, recovered with the help of the mysterious DJ Virgil Vox — also reveals the purpose of the eight extra planets.
In the 100th episode of the series, the crew meets up with Peter, who they eventually deduce will become Drago Museveni, the progenitor of the Nietzschean race.
When she realizes this, her sun enters the Seefra system, and Dylan has to find a way to fix Methus-2 and evacuate eight doomed planets to Seefra-1.
Dylan proceeds with the evacuation of the Seefra planets, although his plans are hindered by General Burma, a religious leader from Seefra-5.
Trance was once the oldest member of the Nebula, but disagreed with their views of organic life as something insignificant and left long ago.
Together with Dylan, she appeals to the Nebula and its leader Maura, who plans to destroy the Abyss by expanding the All Forces Nullification Point until it consumes all galaxies.
When the Andromeda slipstreams to Tarazed, Dylan finds out that only four days have passed since the Battle of Arkology, and the Magog World ship is crippled but still operational.
Andromeda visits Earth (where Harper secretly plans to stay), but as soon as the ship arrives in the system, the planet is promptly destroyed by the Abyss.
After a massive battle with the Nietzscheans of the Drago-Kazov Pride, Dylan checks the Methus Diagram once again and discovers that Trance's sun is capable of destroying the Abyss.
Trance manages to pull her sun closer and plunge it into the Abyss burning it and finally destroying it, as Dylan's battle is over.