The bomb on Scott's chest exploded outward, not injuring him at all. He passed Connolly's test, and retrieves the encrypted data for Section 20 to analyze and unlock, maintaining his cover.
Bratton burns his file on WMD in Iraq. Marshall and Stonebridge deduce that ATAT was planting weapons in Iraq to justify the invasion. How far up the conspiracy goes remains to be seen.
Bratton comes clean to Marshall, but when their meet-up goes awry, Connolly captures both of them. He uses Bratton to gain access to the undisclosed vault containing a secret weapon, then shoots him.
Scott and Stonebridge are able to take out Connolly's men and capture the Irish terrorist and the super-weapon. But when he reveals that he's outfitted Kate with an explosive vest, Stonebridge must decide whether to rescue the mission or his lover.
He chooses Kate and Connolly drives off, then blows her up anyway. The remaining Section 20 tracks down Connolly to Mozambique, and Grant shoots him in the head.