here is my little explanation thingy if it wasn't clear enough:
basically, the whole thing was a plot by sloane to get rid of Irina (who is "first-in-command") but he wants to do it without looking at all suspicious himself. so he manipulates the CIA into killing Irina by having Francie put the "biological warfare agent" into the drink that Syd brings Irina, knowing that Irina will be blamed for Syd's death. However, Syd survives, Vaughn saves her and they stop Irina's execution, etc. So Sloane's plan did not work, and he realizes that Irina/the CIA will be suspicious of him/Francie now, because they want to know who put the biological weapon into the drink.
hmm i think that about sums it up.