The Mothership, or Homeship as it was often called, was the main command vessel of the Taelon Synod. The commander of the vessel seems to also have been the leader of the Synod, at first Quo'on and after his assassination, Zo'or. During the earlier years of the Companion's time on Earth, the Mothership was hidden behind Earth's moon in stationary orbit over the Taelon moonbase. It was uncovered by the Resistance after Paul Chandler and his crew stole a Taelon shuttle to fly to Mars, snapping images of the Mothership and moon base. Later that same year, a Jaridian virus infected the systems of Embassy's around the world, and the Mothership was revealed to the entire world as it appeared to cleanse the Embassy's of the virus.
The Mothership was constructed using core energy, and over the course of it's time around Earth, the Resistance noted that it seemed to grow smaller. This was revealed when the Taelons, several years after it's unveiling, made it known that they were a dying species. Aboard the vessel was a deck entirely devoted to maintaining Taelons in stasis as the core energy crises reached it's pinacle. Both adult Taelons and infants were stored by the Mothership for preservation.
The Mothership survived the final death of the Taelons and the Jaridians, slowly decaying and shutting down after Da'an and the remaining Taelons merged with the final few Jaridians. It became the headquarters of the newly awakened Atavus with the assistance of the traitor, Ronald Sandoval. After Howlyn was defeated and his son took command of the Atavus left on Earth, the last Taelon Raj'el commanded the ship with the other members of the Resistance to leave Earth orbit for good to find the original Atavus homeworld.
The ship appeared first as a armored purple triangular cruiser with thousands of windows. A shield of energy covered it, and could be seen through windows on the inside.
At the beginning of the second season, the mothership changed drastically. The ship was now transparent, glowing with entrails of blue energy that move constantly, it appeared to be larger.
No one knows why the mothership changed so much between seasons. A graphic in "A Stitch In Time" showed that the mothership did have the same shape as the first season version, suggesting that, given the craft's organic nature, it is the same ship having taken a newer form.
The ship contained a control center, with a view out into space, and several corridors above the center, giving a view from above. There was also an observation lounge, smaller than the control center.
The Control Center was introduced as an attempt to make the ship unique. The observation lounge mentioned was used to show the Mothership in the first season. It was not seen later on.