She was present with the rest of the other students when Storm, Iceman, and Beast arrived at their school to let Cyclops know that he needed to be at the reading of Professor X's will. All of the teachers from the New Charles Xavier School decided to go via Magik's teleportation leaving Phoebe and the others behind.
With nothing else to do, Phoebe and her sisters set up a training session in the Danger Room for the others against holographic versions of the Avengers. She participated in the brawl until the program was shut down due to fellow teammate Triage's dislike of who they were fighting.
Phoebe was one of the first to run to Cyclops' aid after he was teleported from South Carolina back to the school by Malloy because of the failed attempt to contact him by Rachel Grey, which resulted in the destruction of a S.H.I.E.L.D. Helicarrier. Scott then had Magik teleport him back to the site as everyone looked on.
The Cuckoos then stood over the body of Magneto after he was transported to the school due to a confrontation between him, Cyclops and Matthew.
As Magneto want on saying that he failed Charles, Phoebe and her sisters read the wayward thoughts of Tempus and her idea to travel back to the past to tell Xavier himself about how screwed up the future has become. They intervened and told her that is the worst idea of all bad ideas.
Later on Phoebe was in a telepathic hive mind with her sisters when they received a psionic backlash after loosing their connection with Emma. As the other students asked what happened Phoebe replied that the new mutant killed Miss Frost.