Let me see if I remember ... Jack thinks Henderson's trying to betray him (of course), and Henderson starts talking to the guy inside about CTU agents being outside and that he, the guy inside, should start dumping out his computer files and get out of there with Henderson. Jack and the others bust in, Henderson claiming that they just came in too soon, that he was trying to trick the guy into dumping everything onto a flash drive. Jack sends the data back to CTU anyway, and Chloe, after a little delay, finds plans for a Russian nuclear sub that just happens to be docked at a more-or-less unguarded dock in the Port of LA. (Apparently, that sub was there being inspected by US forces as part of the treaty Logan had just signed with the Russian president--guess they weren't wasting any time in implementing it). Jack get a hold of the captain, alerts him to the potential attack from Bierko, but it's more or less too late--Bierko and his goons are there, shoot the captain (who's coming topside), and drop the nerve gas canister into the sub, killing everyone on board. I forgot to mention that their goal in getting the ship was a number of (I guess) conventional-but-still-deadly missiles. Jack and a forced-volunteer Henderson are on their way to the site when the show ends. I probably forgot a thing or two in there, but that's the main-story bit.
It was the American naval officer in charge of the inspection who was shot by Bierko while going topside, not the Russian captain of the sub.
