The conversation where Jack convinced President Heller he and Chloe could pull a fast one on the Al-Harazis must have been on a need-to-know basis. It is a lazy turn for the writers, and I'm not too happy about the cheat, but those who picked up on the absence of a silent clock at the end of Hour 8, of course, saw this coming. In Hour 9, thanks to Chloe's tracking, Jack saves the day and ends the Al-Harazi plot, since he now has his get-out-of-jail-free card from President Heller, through the violent technique of defenestration (if you don't know the word, you should have a fun time looking it up!).
This episode provides the wrap-up on the drone plot and introduces the possibility of further trouble when we learn the override could potentially be used to break through any typical firewall protecting the controls of other weapons, American and otherwise. Unaware of Navarro's compromises, Jack brings the override back to the CIA base, allowing for the transition to the next villain plot, led by Adrian Cross and Steve Navarro.
Meanwhile, Kate discovers the assassin killed Jordan. President Heller comes safely back to his staff and daughter, who shows she is still thinking about Jack when she calls him to thank him personally for watching out for her dad. On the other side, Chloe comes back to Adrian, setting up a potential kidnapping or leverage plot later (to hold Jack back when he catches up to them).
This action-packed episode left little time for anything else, like the moral implications of Jack's actions, and showed 24 plots can turn on a dime. Jack's work isn't over.