Theron Shan and Lana Beniko
When the Alliance was formed, the intelligence came from Theron Shan and his agents within the Republic Strategic Information Service, as well as Imperial-Alliance sympathizers from Lana Beniko, and contacts throughout the galaxy.
Intelligence was often working on how to disable the Eternal Fleet from the Arcann and Vaylin. Many efforts led to the discovery of pro-Alliance agents and valuable resources. A notable mission was the detection of a Hyperwave frequency under the Spire on Zakuul, which sent and received orders to and from the Eternal Fleet. While the mission was technically a failure, it did reveal information on GEMINI Prime, eventually leading to events that drastically changed the war.
The first task of Alliance Intelligence was to combat a series of uprisings that threatened the stability of the Alliance and peace between it and the other powers of the galaxy. Their efforts stopped a number of incidents, including a plan to frame the Alliance of a bombing the Senate Building on Coruscant, as well as revealing anti-Alliance elements within the Republic and Empire.
Later, intelligence agents were given the duty of learning about the Republic and Empire and their motives on Iokath. After an incident on the planet, they were tasked with finding the traitor who attempted to murder the Commander.
Theron Shan leads the Commander and Lana into a trap on Umbara.
Eventually, after the war on Iokath, intelligence received from an anonymous source that the traitor was on board of an Umbaran supply train filled with Adegan crystals. The Alliance Commander traveled to Umbara before Intelligence could confirm it, although director Shan gave his input and agreed to engage the train. The Commander, along with Theron and Lana Beniko, boarded the train.
The trio eventually reached the train control room, were Theron Shan opened fire and revealed himself to be the traitor stating that he was part of an effort to destroy the Alliance. Eventually, the Commander and Beniko escaped and they returned to Odessen. After the missing Lana Beniko took over as the temporary director but didn't have all of the duties her predecessor previously had.