After Elliot filed a release form for Hank Roberts and secretly gave his step son Nicky his business card, Don ordered Elliot to stay away from the Roberts family.
Elliot: I'm going home, Captain
Karen Stern's twitter, there was more to the scene with spoken dialouge between Elliot and Kathy. Kathy was being supportive to Elliot. However, Karen (as well as the crew- Dick Wolf, Neal Baer, etc) felt that the scene was more powerful with Kathy checking in on Elliot and Eli, so the extended scene was cut.
This episode would be the last appearance of Eli