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The motherships were conceptualized by Juras, and the prototype Moratun was held in high regard by him. The ship was sent on an extended search for sentient life after the Kalath Intercession with Juras as its sole crewmember; Juras was placed in stasis, to be awakened when the mothership encountered sentient life.
In 2500, after many centuries of uneventful journeying, the Moratun and the other dormant motherships received a cryptic message from Aiur ordering them to return home; although not elaborated in the message the protoss homeworld was overrun by zerg and the surviving protoss were summoning the ships to reinforce the war effort. Juras was awakened and began piloting the ship back.
The Moratun stopped by Samiku for a course adjustment and to take on crew. The planet's protoss outpost was being overrun by zerg and the ship rescued besieged Templar forces. The Templar, led by Commander Martul, formed a skeleton crew. The pacifistic Juras was at odds with Martul over the use of the ship's weapons.
The ship traveled to Aiur and was attacked by zerg aerial strains as it entered the atmosphere. The shields began to deplete but, to Martul's consternation, Juras refused to unlock the ship's weapons. Juras' belief that peace was possible with the invaders evaporated after witnessing the death of a Khalai Caste survivor on the planet surface. The weapons were finally unlocked and the Moratun began picking up what few survivors could be found.
The Moratun joined the mothership fleet assembling near Aiur, and together went to find the unknown place the refugees had fled to and rejoin protoss civilization. They were occasionally attacked by zerg leviathans which the mothership fleet easily destroyed.