They were just half the team that went in - she couldn't catch the other two.

While it's impossible to tell what she's doing, she must have a plan, since she's me on some level. If Twilight is fighting to take her body back from Cálice, she's probably in... let's call it Inner Canterlot, since it's inside her. The other two that went in said they were feeling a strong pull from that direction.