Emperor Zetch'r'r

There's a lot more on recent githyanki politics (as far as the Scales of War adventure path goes) in Dragon #377's article on Tu'narath.

1. Interestingly, they don't blame Gith for the civil war. "For a time Gith tolerated Zerthimon; she would not see the freedom she had won dashed with a new tyranny, even if tyranny was for her own people’s good. Her followers did not share her patience, however, and soon heated arguments erupted into open violence to silence the voice of opposition. Before Gith could react, the sporadic skirmishes exploded into civil war, and once started it appeared that it would find no end until one or both sides were destroyed." That's the most charitable (to Gith) interpretation I've seen. More charitable to Zerthimon than some interpretations, too.

2. We learn exactly what happened to Gith. Gith negotiated with Dispater first, but was unable to agree to his price (the souls of all githyanki). Dispater introduced her to Ephelomon, and Gith was held hostage in Dis as a guarantee of good faith. She remained there for millennia, her mortal body dying but her spirit imprisoned as long as the pact with the red dragons remained in force. Vlaakith I was apparently actually Gith's named successor (that is, Vlaakith wasn't lying about that, as I had suspected).

3. The Scales of War adventure path takes place 25 years after "The Lich-Queen's Beloved" in Dungeon #100. "The adventure path takes one possible outcome and projects it 25 years into the future."

4. Zetch'rr and his Sha'sal Khou faction lacked enough popular support to seize control after Vlaakith's death, and worse, Zetch'rr was suspected (correctly) in having a hand in the regicide. In desperation, Zetch'rr went to Tiamat and renegotiated the terms of the pact, swearing the undying allegiance of the githyanki race (an oath Gith had refused to give). With the aid of Tiamat's armies, Tu'narath fell in a single day, and Zetch'rr was crowned emperor. Zetch'rr had hoped to outwit Tiamat and continue the Eternal Crusade against the illithids, but Tiamat got the better of him and began treating the githyanki as her slaves.

5. With the original pact broken, Gith's spirit was finally freed from the dungeons of Dis. Gith returned to Tu'narath to take charge of the city and fix everything, but before she could possess Zetch'rr as she had planned, her spirit was accidentally snared by a young female ghustil. Gith annihilated the woman's spirit and took over her body, but with her relatively low caste she was now unable to take control of Tu'narath without help. This means that the knight who called herself Gith Reborn in Vortex of Madness must have been simply delusional.

6. Gith, in the ghustil's body, began claiming to be Vlaakith (presumedly Vlaakith CLVII, the lich-queen) reborn. Apparently she thought she'd be more influential as the recent queen than as the legendary founder of the race (or maybe everyone was just sick of people claiming to be the reincarnation of Gith). She became leader of the Ch'r'ai faction of Vlaakith-loyalists, and also gathered disaffected members of the Sha'sal Khou faction that Zetch'rr had previously headed, and oppressed workers and so forth that were angry with Zetch'rr.

And that sets up the background of the adventure path, I guess, Zetch'rr as reluctant tyrant enslaved to Tiamat and a reincarnated Gith (posing as a reincarnated Vlaakith) as the head of a powerful rival faction seeking to topple the government.