UAJ hoped to provide an alternative separatist movement to the MNLF. UAJ used his personal relationships with Al-Qaeda to conduct high visibility attacks on Christians in order to secure funding and gain international recognition until he was killed by police on 18 December 1998 [2]. The AFP conducted several counter-terrorism operations after UAJ's death and removed several key ASG leaders from the battlefield [5]. The ASG turned to kidnap for ransom in lieu of terrorist attacks to create a better revenue stream after being weakened by AFP operations [5]. Khadaffi Janjalani (KJ), UAJ's brother, used the power vacuum to consolidate power [5]. KJ utilized a strong personal relationship with JI to bring in new operational funding and training which allowed a return to high profile attacks [5]. KJ was killed in September 2006 during a US backed operation, Operation Ultimatum, that resulted in six notable ASG leaders and hundreds of fighters being killed [5]. The ASG has lacked a definitive command structure and operated more as a loosely affiliated criminal enterprise that depended on its top five to six leader since KJ's death and the 2007 counter terrorism operations [2]. .

             Ismilon Hapila led ASG's most important cell in Basilan but was rendered ineffective by 2002 operations [2]. This led to many Basilan based ASG members transitioning to the Sulu Islands under the leadership of Radullah Sahiron (RS), also known as Kummander Putol, making RS the defacto leader of the ASG [2].

             Radullah Sahiron was originally a member of MNLF but distanced himself from the leadership following 1986 negotiations with the Philippine government [2]. Radullah joined the ASG in the mid 1990s when UAJ sought sanctuary on Jolo Island [2]. Radullah married UAJ's widow bringing the Sulu and Basilian sections of the ASG closer together [2]. Radullah is described as a charismatic leader that has been able to maintain loyalty within the ASG and from more militant factions of the MNLF [2].