As an image of the 9/11 twin towers is shown in "Storm Front, part two," Daniels says, "it's almost ready," in reference to the timeline resetting itself.

DANIELS: It's quite a sight. The timeline's resetting itself. You did it. Vosk is dead. He didn't make it back. All of the damage he caused, it never happened.
ARCHER: And you're here to give me a pat on the back.
DANIELS: In a way.
ARCHER: Well, I don't want it. I want you to leave me and my crew alone. We're done with you and your damn Temporal Cold War.
DANIELS: It's coming to an end because of what you did. You have no idea how many lives you've saved.
ARCHER: I'll take your word for it. Just send us home.
DANIELS: It's almost ready. Good-bye, Jonathan. Captain. It's been a privilege.
ARCHER: And you're here to give me a pat on the back.
DANIELS: In a way.
ARCHER: Well, I don't want it. I want you to leave me and my crew alone. We're done with you and your damn Temporal Cold War.
DANIELS: It's coming to an end because of what you did. You have no idea how many lives you've saved.
ARCHER: I'll take your word for it. Just send us home.
DANIELS: It's almost ready. Good-bye, Jonathan. Captain. It's been a privilege.