While Elena was busy taking care of Haruhi and her soul, a group was starting to surround the cage, inside which she was doing the treatment. As soon as she had broken in and killed the men inside, the people present in this secret base had immediately noticed her presence.
Even though Elena had killed all three of the men abusing Haruhi effortlessly in her rage, one of them was actually the third strongest person present in this place. That was why, even after Elena's presence was discovered as an intruder, people had not rushed inside the cage to kill her. Instead they were surrounding it to make sure that she was not able to run away.
As the people surrounding the cage were looking at it with fearful eyes, three people with an authoritative air around them came inside this room. From the way they were dressed, it was clear that all of them had a high standing here.