What happened to Sark this episode is almost exactly what happened to him in Season 2 finale; from being jailed to getting his face broken by Vaughn.
Sydney's full name is revealed to be Sydney Anne Bristow.
Number 47: The initiation date of Project SAB47 is 04/17/75 (Sydney's birthday).
Number 47: On the same document there other references, such as "NO. 938 JB/47" and "176847."
Number 47: On the document that Sydney read in the end was a name for the project "S.A.B. 47 Project."
Number 47: (hidden and reversed) Hank Foster says that Sydney was logged in at the safe-house where Nadia was being held at 7.22 p.m. (2+2=4; =74).
When Lauren points the gun at Sydney, she tells Vaughn "if you love her, you'll put the gun down". This same situation also happened in "Blowback," except that it was Sark who was pointing the gun.
When Vaughn uses the key to Jack's storage shed he grabs a rifle with a scope, Vaughn takes off the cap on the scope and then looks through it, however it would be impossible to see any thing because he didn't take off the second cap at the other end of it.
As Vaughn is escaping the hospital he pulls the folded firehose from its storage case. The next shot shows a nicely rolled hose falling down the stairwell.
When Sydney took the clip from Katya, there was no bullet chambered. Even if she left the clip in there would have been no bullet fired.
If you remove a full ammunition cartridge from a gun and hand it to someone, the weight will give away that the gun is empty.
EMTs wouldn't move someone stabbed in the back and suffering from a punctured lung, on their back on a gurney. Yet that's how they move Vaughn when they bring him in.
We have every reason to believe that Sark hacked into the CIA security feed when Lauren was infiltrating the rotunda. When on a view of the feed on Sark's laptop you can see the point where Lauren takes her Sydney mask off, meaning if the CIA has all of the feed there would be proof that it was Lauren and not Sydney who stole the equation.
The CIA investigators probably already knew the one inside rotunda wasn't Sydney, otherwise, they would have taken more severe actions than just questioning her. Their main suspicion stemmed from Lauren and Sark knowing Sydney wasn't in the facility, thus pulling off their fake Sydney infiltration; they wanted to know why she was conveniently away during the attack.
Marshall noted that CIA paid him very well, though less than one million dollars a year.
Why would Sloane put his entire collection of Rambaldi serum out in the open where it could potentially be compromised? It's been established that Sloane is not dumb and well versed in Game theory. Even a novice in Game theory or contingencies would keep something that valuable in a spot that isn't easily reached or at the very least, easily compromised/broken, yet Nadia is able to destroy them quickly and conveniently.
If The Passenger was already known to the Russians, and they did experiments on her with the Rambaldi serum, why did everyone go through the trouble of collecting the Rambaldi artifacts to build "Il Dire", that's the final machine that gave Sloane the word "Peace" and generated the genetic code in "Unveiled". Also, some of the artifacts used to build "Il Dire" where hidden and untouched for may years so how did the Russians know who the passenger was and what she represented?
When Vaughn, Sydney and Katya are driving away from the checkpoint outside of Novgorod 12, you can clearly see palm trees in the background. No species of palm tree grows in Russia.
How does Vaughn know there was acid in the beaker? He just picks up a glass rod and dips it in the acid, then puts it on Suit & Glasses. But the beaker is unmarked, and they didn't have a chance to see S&G use the acid.
Going into someone's safehouse and putting your fingerprints all over their secret cache of untraceable weapons isn't really a good idea. If Jack were to use one of those weapons down the road to kill someone, then Vaughn's fingerprints would be on them.
Why did they give Toni a gun for the break-in mission? Given she's a prisoner out on parole and all, and she really only needs to get in to deactivate the security system, arming her seems like a real dumb idea.