I usually hate seeing Sydney crying, but I'll excuse her for this episode.
Sydney always had an idealised view of her mother since she learned that she was a spy - Irina was bad, but she always loved Syd. And Sydney always trusted/loved Irina more than Jack.
It turns out Syd was wrong. Jack learned that Irina had put a contract out on Syd so Jack had to killl Irina in order to protect her. He had no other option.
This is great writing because it is consistant with everything that we know:
1. Jack loves Syd and would do anything to protect her even if he has to sacrifice himself.
2. Jack wasn't a cold blooded, vengeful former husband fed up with Irina's betrayal
3. Syd has poor judgment in the people that she loves - Jack, Irina, and Vaughn.
4. Sloane is Jack's friend even though they see things differently.
5. Sloane cares for Sydney.
6. Irina previously showed that she was willing to kill Sydney if she had to. Something undisclosed happened that forced Irina to take action. I suspect that it was the prophesy that the Chosen One and The Passenger would battle and only one would survive. Irina must have been hoping that Sydney and Nadia would never meet, so that would have prevented the prophesy. Irina must have worried now that Syd and Nadia had met, the prophesy would happen. Irina must have wanted Nadia survive more than she did Sydney.
onder:
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