There were at least two Gallifreyan Civil Wars, both engendered by Pandora.
One happened when Pandora tried to make Gallifrey use its temporal power to change the Web of Time for her own ends. She was captured and dispersed so completely that she never existed. However, a portion of her consciousness survived in the Matrix. Over time, Pandora gained strength and tried to escape. This was prevented by Leela and K9 Mark II, though this left Romana II unable to access the matrix. (AUDIO: Lies)
However, Darkel later released her, aiming to use her release to remove Romana from the presidency. Irving Braxiatel took the past and present forms of Pandora and went into exile on his collection. (AUDIO: Pandora)
Romana took to consulting her due to Darkel's attitude to Romana's policies, through K9 Mark II. During the election following Darkel's right of contest, Romana declared herself Imperiatrix. Whilst K9 was inhabited Pandora there was a terrorist attack on the chapter houses of Gallifrey and the High Council, Pandora tricked Romana into accessing the Matrix and escaped it, using the form of Romana's first incarnation. This led to the next civil war. (AUDIO: Imperiatrix)
During the war, Pandora force-regenerated many Time Lords in order to swell her forces, while Romana destroyed the infrastructure of the planet. Romana also scrambled the Rassilon Imprimaturs of TARDISes to stop the war becoming a time war. It was during one such attack that Narvin was injured and Leela lost her sight. Romana and Hallan went to the Anomaly Vaults to find Wynter's TARDIS but found Aesino, a weapon the Celestial Intervention Agency was planning to use in their missions. Romana then became linked to the sentience that controlled the vault when she escaped from the vault. (AUDIO: Fractures)
From their base in the Time Lord Academy, Romana's allies fought back against Pandora and Darkel. Darkel placed a bug bomb on Narvin in order to try to get him on her side. Unbeknownst to Romana, Pandora had created a technological variant of the Dogma Virus which she planned to used to convert all the Time Lords to her will. Romana planned to use the Matrix against Pandora. Capturing the APC Net, she tricked Pandora into entering a Matrix partition and used the sentience to drag her back into the Dark Partion of the Matrix. Romana then destroyed the Matrix to prevent her reappearance. (AUDIO: Warfare)