Plot (as far as I can remember. or understand):
1. Jason Bourne rebels against treadstone.
2. Ed Norton and gang pull the plug on their other programs fearing another rogue agent (a-la Jason Bourne). Begins terminating existing agents
3. Jeremy Renner escapes termination by getting rid of tracker in his thigh (or abdomen).
4. Ed Norton and gang wipes out science team to clear "evidence" of program existing. Rachel Weisz escapes.
5. Jeremy Renner learns about science lab massacre through newspaper. Finds Rachel Weisz.
6. Jeremy offers Rachel protection. In return, asks Rachel Weisz to develop counter-virus to eliminate his dependency of life-sustaining "agent pills".
7. Jeremy and Rachel go to Pinas to develop cure. Rachel injects Jeremy cure. Cures Jeremy.
8. Story ends.