Abbott Elementary season 3 shocked us with the reveal in the premiere, "Career Day," that Janine was no longer teaching at the school. Now, it's only a temporary move, but it does mean that she isn't there for the day-to-day happenings at the institution though she still will have a presence. This is because Janine accepted a fellowship offered by the school district which gives her the opportunity to work with its representatives to help improve the schools in the area.
Janine has always wanted to be a force of good for her community. She's done so at Abbott but this is a chance to do more not only for her students but the rest of the children being educated in the district. At first, she was hesitant when Manny said that she'd make an excellent candidate. For so long she's been used to her ideas being dismissed but he listened to her and felt that what she had to offer in the way of her ingenuity, creativity, and desire to change what's wrong with their school system was worthy of being pursued.
After encouragement from Barbara and Jacob, Janine felt like it would be the right decision for her to accept the fellowship even though she'd have to leave her kids. Gregory, however, wasn't as enthusiastic because he never thought she'd leave Abbott. He admitted that when he thinks of Janine, he thinks of the school and vice versa.
Five months later, with Janine firmly in her new position with the school district, it's revealed that she had tried to see if she and Gregory could start a relationship. But he said it would be safer if they remained friends. When she said they couldn't be together because she needed to choose herself instead of beginning a romance, he'd respect her decision and worked through his feelings to move on during the summer break. He didn't want to re-open that door so things were left awkward between them.
At the end of "Career Day," Janine and Gregory talked about that conversation in order to clear the air between them. Gregory had been under the impression that she'd left Abbott because he'd rejected her advance but that couldn't have been further from the truth. She took the fellowship because it was what was right for her. With that sorted, the two are friends once more though we do expect complications to arise since they have feelings for one another even though they aren't going to explore them.
It's unknown when Janine will return to teaching at Abbott Elementary, but we do know that she still sees her class as her own even though they're being educated by a substitute. The teacher does things differently from her and has different tastes, it'll be interesting to see if that continues to be a problem as the season goes on. As you can see in the image below, they don't have a warm dynamic.