Don't be confused, I've figured it all out!

Rating: 6/10 (25 August 2012)

Spoilers Galore:
Aaron Cross (Jeremy Renner) dives under a waterfall in Alaska and retrieves a cylinder tethered to the bottom of the stream. Why? What was in it? We'll never know. He then crosses across mountain tops, occasionally swallowing important blue and green pills.
We can assume he's on some sort of mission. He eventually reaches either a rendezvous point or his final destination. There he meets another operative or contact and they banter back and forth, clearly confusing each other until Cross tucks in for the night and notices the name "Jason Bourne", among others, carved into a board above his head.
Meanwhile, back at the CIA, we realize Bourne has exposed treadstone and blackbriar effectively killing those covert programs. "Colonel" Byer (Edward Norton) has some kind of big job in intelligence ... big enough to order the elimination of all covert agents associated with these two programs. We find out these agents are referred to a "outcome assets." Aha, Cross must be one of these guys!
Back in the Alaskan cabin, Cross is ready to move on. He steps outside into an oncoming blizzard and hears an airplane engine. It's a drone. He and the other spy-like guy are paranoid and not expecting a drone so they decide to split up. Cross runs out into the blizzard just as the drone launches a missile at the cabin. Cross outwits Byer and the killer drone squad and is assumed dead. (This was not at all confusing and one of the better parts of the movie!)
Meanwhile, back at the lab (the one that makes blue and green pills), one scientist goes "postal" and murders all but one of his coworkers. The survivor is Marta Shearing (Rachel Weisz) who has previously flirted with Cross when he visited the lab for check-ups. He's hot for her, she only knows him as "number 5".
Five minutes or five days later, Cross is in Chicago and talks to someone on a phone, then Marta is attacked at home by CIA assassins. Remarkably, she is saved by Cross! While escaping the massacre at Marta's home, Cross and Marta FINALLY discuss the blue and green pills. One of them makes you smarter and one of them makes you stronger. Marta explains that if you "attach" the drug to a virus and inject that into a spy, he won't need the pills to be a super spy anymore. Unbeknownst to Cross, he was already "viraled out" on the muscle pill a year earlier!
Cross reveals to Marta that he was not originally one of the smartest "outcome agents" in the club and he'd like to retain his enhanced brain power! She's cool with that so they fly off to Manilla to get some brain power drugs. If he doesn't get the drugs soon, he'll die or get sick or go crazy or just get stupid again ... it's not real clear.
The CIA is not stupid. They use every trick in the "post 911, so it's okay to spy on our own citizens" book to find Cross and Marta in Manilla but it's too late, Cross is now permanently smart. So smart and strong that he's able to evade another top secret "super duper spy," Larx-03. Larx-03 is relentless and must have read the script because it's impossible for Cross to shake him in the crowded streets and neighborhoods of Manilla. Eventually, during a motorcycle chase, Marta, manages to kick Larx-03 off his bike allowing her and Cross to escape.
Then Joan Allen's "Landry" character is seen back in the states being arrested or facing a senate committee or facing the media, honestly is was so out of left field, I could't wrap my head around it!
Cross and Marta are last seen, James Bond style, sailing away from the Philippines on a rickety old fishing boat ... the end ... really, that's it!