The CIA manage to locate Aaron Cross (Jeremy Renner) and Marta Shearing (Rachel Weisz) in the Philippines, where Aaron is able to viral off one of the drugs he was taking to help improve his mental and physical conditions. Despite recovering from the viralling off the Manila police close in on his and Marta's location while she is out buying medicine. The two then manage to escape the police and escape on a motorcycle navigating the clogged city roads. They then encounter another person chasing them (Larx-03) that is not a member of the police force but is a similar agent to Cross. A chemically different agent who lacks emotional attachment and is more easily controlled. Both Larx-03 and Aaron are shot by one another during their pursuit.
Closing in on his targets, Marta manages to help crash Larx-03 in a factory presumably killing him and manages to help a wounded Aaron crash safely before being discovered by a local fisherman. The two are then on a fishing boat looking over the maps of the region and not knowing exactly where they are, content with that fact.
Thanks James C!