Talk to Tarkis Arri and her inner council. She offers you her fealty and the loyalty of her men as officers of the Court under your authority (Yeomen Wardens in local parlance). If you want to start the Rebel questline, do so. Alternatively, you can betray the group and attack the rebel leaders.
Return to the Disfavored camp and attend the meeting of the Archons. Choose either Archon to lead the charge, fomenting dissent.
Travel to Vendrien's Well Citadel and talk to Tarkis Arri. Your Fear with Eb and Wrath with Vendrien Guard will receive a major reduction. You'll also receive a bonus to your Loyalty and Favor with the same. Eb will also join your party and become available for deployment.
Before you leave Arri, you can ask her about the deal involving Disfavored prisoners. This will not count as evidence against Ashe in A Trial of Archons if Nerat outs himself for consuming Ashe's son.
Return to the entrance. The Chorus under Fifth Eye breaks through, leaving a small rear guard for you to defeat. Deal with them, then head into the barracks. Fight your way through the Chorus forces to Ascension Hall.
Confront Fifth Eye. The situation mimics the one during Assault on the Citadel and your choices are similar. You can use Lore to get rid of the Blood Chanter, Athletics to get rid of the Scarlet Fury, or bluff and make them all weakened. You can also invoke Betray Alliance and begin the anarchist path.
You automatically claim the spire, ending the quest.