The Underground was a rebel movement in Haven City introduced in Jak II. They were united for the cause to dethrone the de facto ruler of the city, Baron Praxis, and reinstitute the House of Mar as the ruling dynasty. The Underground was led by the Shadow and Torn, and was headquartered at the hideout in the Slums.
Before Jak II
It is unknown when exactly the Underground faction was formed, or by whom, though it was formed sometime after Baron Praxis came to the throne after banishing Haven City's former king, Damas, to the Wasteland. Damas' son, Mar, was the heir to Haven City's throne, though due to the ongoing war, Baron Praxis was able to convince Haven City they needed a "strong leader", and thus came to throne. A man named the Shadow led the Underground before and during the events of Jak II, and possibly founded it. Torn, a former Krimzon Guard captain, also became a high-ranking and important member of the Underground.
The Underground was first introduced in Jak II after Jak and Daxter protected Kor and "the kid" (the heir to the throne) from a squad of guards. Kor directed them to go to a dead-end alley near the city wall and ask for Torn. Torn was not interested in Jak and Daxter's membership, and had apparently already received word that Jak and Daxter wanted to join the "fight for the city". As an initiation test, Torn gave Jak and Daxter the mission "Retrieve banner from Dead Town", in which Jak had to fight his way through the city ruins of Dead Town up to the Baron's ruined tower, remove his ensign, and bring it back to Torn. Jak and Daxter successfully accomplished the mission, and were therefore admitted to the Underground.
From that point forward, Jak and Daxter completed various missions for Torn, including delivering payment for a supplier to the Underground, rescuing an important Underground informant, protecting an Underground spy, and many more. Jak and Daxter completed several missions for the Underground before finally meeting the Shadow, at which point they discovered he was a young Samos Hagai. When the Shadow and the child heir went back in time to Sandover Village, older Samos Hagai, from the past, superseded the Shadow's role in the Underground, thus continuing his station as a fighter for the city.
After Jak II
After the death of Baron Praxis, Underground spy Ashelin Praxis, the Baron's daughter, became the governor of Haven City. They disconnected from the child heir after he was sent back in time. Therefore, Ashelin became the next-in-line chairman of Haven City. The Krimzon Guard was dissolved, and the Underground as well due to the fact their mission statement became obsolete. The Underground and the old Krimzon Guard merged to form the New Krimzon Guard and eventually the Freedom League. Samos Hagai, who continued his role as leader, became an important member of the Freedom League, and Torn continued his role as captain of his soldiers.
The Underground is identifiable by its obvious rebellious emblem, containing the coat of arms associated with the rule of Baron Praxis, but with a hammer on top of a cracked skull and dripping paint, giving it a "graffiti" theme, with a green backsplash.
There were numerous "men" working for the Underground, all rebels, and did not appear to have any uniform associated with them, making them hard to identify. It was even hard for the Krimzon Guard to find Underground "fugitives", as they would hold everyone within a sector or district under arrest for suspicion of harboring Underground members, and would try other tactics to run Underground members out such as shutting off all plumbing to the Slums, where the Underground hideout was located, deploy mobile bombs in an attempt to kill Underground members, and would also pursue and apprehend any civilian which gave off a slightly suspicious impression. In the mission "Shuttle Underground fighters", all Underground "fighters" wore the same green sweater, beige pants, and red bandanna over their mouth, suggesting members under the "fighter" status wore similar uniforms, though this cannot be confirmed.
The Underground primarily gathered at the hideout which was a small bunker located near the city wall in the Slums. This is where Torn, the Shadow, Kor, Jak, and the rest of the Underground movement plotted their actions against the Baron. Escorts also took place between the hideout and the power station where Vin and Kor were located.
The Underground had various third-party connections which allowed them to gather intel on the workings of Baron Praxis. Vin, described as "one of the Underground's best informants", was the frontman and engineer for Haven City's defense and eco grid. After Jak rescued Vin at the strip mine from the metal heads, he assisted Jak and the Underground in their rebellion. The Underground also had connections with Krew, a bar owner, arms dealer, crime lord, and smuggler, who was a freelance weapons contractor and also worked for the Baron at a price. Ashelin Praxis, the daughter of Baron Praxis and Krimzon Guard comrade, also served as a spy for the Underground, gathering information and relaying it to Torn. It was also made apparent that the two were in a relationship of some sort.