While arguing with the handmaids at the diner, June realizes that Emily isn't around. Nobody seems to know where she is. The argument escalates, and one of the handmaids fires shots into the air. They all rush into their cars and drive off. June heads to Emily's to find out what happened.
Sylvia, her wife, comes out and tells June that Emily left to go to Gilead. She wanted to fight, maybe find Aunt Lydia. It was what Emily had to do. Emily called to say that she was leaving, but she wouldn't say goodbye to their son, Oliver. Sylvia seemed shocked by that.
In season 4, June forced Emily to confront Aunt Irene, who was responsible for the death of her former lover, a martha. Emily refused to forgive the woman and later found her hanging from a tree. Irene was so fraught with guilt that she committed suicide, and Emily loved it. It brought out her old sadistic streak that defined her character in Gilead, which was exactly what June had intended. It's the reason Emily attended Fred's salvaging.
We realize that instead of having Emily take part in the fight onscreen, which we expected, they used her newfound mindset to send her on a reckless journey across the border. It was a way to make up for Alexis Bledel's departure from the cast.
It's assumed that she will die and that Sylvia will never see her again. We might not hear about her death, but that is most likely going to be her fate.
This is when June starts to feel guilty. She pushed Emily to go back to her old, brutal self and it sent her to her death. Sylvia stops her and says that she doesn't need it to be anyone's fault. She doesn't want to be mad. She wants to cherish the time she had with her wife and move on.
At this point, June could never accept that mindset. She's too upset at herself. She asks Sylvia to tell her if there's any news. Sylvia refuses and tells her goodbye. Likely this will be the last time we hear anything about Emily. It was scathing, and it's a shame that such an amazing character had to exit with nothing more than an angry goodbye.
Some people say that it was a sloppy solution to Bledel's departure. Emily might have been a killer, but she wasn't reckless. I highly agree.
June gets back in her car and finally realizes that there's blood on her hands. Her actions had consequences. Someone she loved is going to die, and she's responsible for it.