So last installment's cliffhanger turns out to not be such a big deal. Success Shep managed to overlook Liara's infodrone Glyph, who proceeds to open all the vaults the squad members are trapped in. Fail Shep, EDI and James go to reclaim their ship. Taking EDI along proves to be a somewhat bad idea, as CAT6 cuts her off from the Normandy's systems, which messes up her mind. Luckily, all this does in gameplay terms is remove the glowing visor she wears.
Success Shep really wasn't expecting Fail Shep to escape the Archives and it shows. CAT6 presence on the Normandy's dock is minimal, the comm jammers that CAT6 has been using to prevent Citadel Control from stopping their takeoff also prevent them from using comms to call for reinforcements, cutting off EDI from the Normandy has disabled most of the ship's security systems, and Success Shep has gone into the "NO, I'M THE REAL ONE!!!!111" phase of Cloning Blues.
The squad arrives at the Normandy's docking hatch to find the main door locked and Traynor pissed about being fired by Shepard. James explains to her what's going on ("Shepard has a clone. Yes, I know that sounds stupid") and Traynor uses her toothbrush (it uses mass effect fields and costs 8,000 credits) to save the day.
I like that Bioware actually accounted for whether Shepard knows about Traynor's toothbrush. If you never asked her about it, she explains it here. Kind of ruins the Brick Joke, sadly.
The squad fights their way through the Normandy CIC and makes their way to the cargo bay, where they find Success Shep in a white and blue version of Fail Shep's default armor. Thus begins the best boss fight of the trilogy.
The clone's abilities are based off of Shepard's class. Since Fail Shep is a soldier, Success Shep uses an assault rifle and Incinerate (even though soldiers cannot learn the latter.) You have to deplete Success Shep's health meter five times: this is justified by his using medigel every time he gets low on health. You also have to deal with Brooks (whose only real techniques are cloaking and automatically reviving herself a few seconds after her health is depleted) and CAT6 reinforcements.
Once Success Shep uses up half of his medigel, a cutscene starts where Cortez and Joker drive a skycar in front of the Normandy to prevent the ship from going to FTL. Joker knows about the Normandy's blindspots, so CAT6 has to resort to sending the Kodiak to take the skycar out. But Cortez knows his own shuttle too well for that to work.
This cutscene opens the Normandy's hanger doors and when Success Shep's health is depleted for the last time, he and Fail Shep go tumbling out. James and EDI go to their friend's assistance, but Brooks leaves Success Shep to his fate. Fail Shep kills himself and lives to tell the tale.
Joker and Cortez capture the Kodiak and arrest its pilot (who is incidentally the sole survivor of CAT6). Fail Shep tries to take Brooks into custody, but she breaks out of her handcuffs and James shoots her dead.
The Normandy returns to the docks and the squad turns over their prisoner to C-SEC. With the crisis resolved, there is only one thing left to do. The only thing that makes sense when the entire galaxy is fucked.
Party.