The Yehat Rebellion, also called the Yehat Revolution, is a civil war between the Yehat Rebels and the Yehat Royalists. It is an optional event that only occurs if The Captain restores the Shofixti race and proves this to the Yehat Starship Clans.
 Seeds of rebellion
The Starship Clans were ashamed of their actions in the Great War, particularly when obeying the orders of the Veep-Neep Queen to abandon the Shofixti to the Ur-Quan Kzer-Za at Delta Gorno. The Starship Clans knew that if the Shofixti were still alive, the shame would be unbearable.
The Captain can meet with the Yehat during Star Control II, but while they are sympathetic to his cause, the Queen gives direct orders to the Starship Clans not to give him any assistance. This changes when The Captain revives the Shofixti race and sends a Shofixti captain to meet with representatives of the Starship Clans. The shock of seeing their adopted children reborn forces the Yehat to face their shameful actions, and in response, the Zeep-Zeep Clan declares war on the Veep-Neep Queen.
 Events of the rebellion
The civil war begins with both sides in control of roughly half the total star systems under the original Yehat sphere of influence.
The Yehat Rebels eventually defeat the Yehat Royalists and pull the Veep-Neep Queen from the High Perch. Surprisingly, Braky Girdy the First, a Pkunk, flies in to replace the Veep-Neep Queen and unites the Clans "in peace and harmony as never before."
The peaceful Pkunk successfully absorb themselves into Yehat culture and begin to provide the Yehat with spiritual insights into themselves. The combined Pkunk Fury and Yehat Terminator fleets provide The Captain with some much needed reinforcements after he fights through the Ur-Quan Kzer-Za and Kohr-Ah defenses to face the Sa-Matra.