The Phantom is one special ghost! We saw back in Chapter 9 that he's not affected by the Ghost Rules, like when he pulled Cyrus up through the floors of the castle. So, unlike an ordinary ghost, the Phantom can come and go from Thantopolis as he pleases. Though that doesn't explain why he's here now...

Helene told Cyrus that apocalyptic tidbit way back in Chapter 1. When the Orinthope is not contained by Helene's power (or channeled through the power of a medium), it's indiscriminate in what it sucks up.