Much of these changes revolve around the Machine, and who is actually in control of it:
"We're so used to thinking of the machine in one way — as the ever-present source of information in the background. It's sort of omniscient but definitely under the control of its builders and operators. I don't think anyone has ever considered that the machine was capable of independent activity. I think that's a notion that comes up before we're done."
Emerson confirms that tonight will see the return of Root, the hacker who attacked the Machine earlier this season, and who will become a deeper threat to Finch:
"In her, he has an adversary more dangerous than he ever dreamed. I think he thought she was an extremely clever, almost attractive hacker. ... [But] she's going to come after him in a shocking way, a personal way. She's not going to seem nearly so charming anymore."
But Finch isn't the only one in danger. His and Reese's entire operation could come undone, and the writers will keep us guessing until next season as to how our heroes will prevail:
"Something unprecedented happens at the end of the finale. It's a great cliffhanger and it will determine everything that happens for quite a few episodes when we come back in Season 2. The real physical danger will surprise the audience, and the audience will be left thinking, 'How can they go on doing what they do?' The circle must be broken, the audience will feel."
Be sure to tune in tonight at 9 pm on CBS.
Source: TV Guide