A few theories, some more plausible than others:
1. Stan's gf is an American spy, not a Russian, sent by the CIA to track him as a potential defector (Sub-theory: maybe they suspect P&E and know that he's friends with them).
2. Stobert is fully aware of Elizabeth's spy status and is playing her. His bit about developing super-wheat that is pest/famine-resistant was a trap, knowing that she would steal it.
3. Paige continues to connect her religion's "all for one, one for all" premise with the communist manifesto. She moves toward the life of a spy, much to the joy of the Center and the chagrin of P&E, who actively try to keep her out.
4. P&E are going to be asked to take down Stan and Dennis' defector and the resulting confrontation will conclude this season.