At some point in the past on Earth-9997 both Havok and Polaris left Earth to join Havok's father, Corsair, in outer space. Although their reasons for leaving the Earth remain unrevealed at present time.
Polaris, Havok and Corsair at one point pleaded with Scott Summers (Corsair's son and Havok's brother) to leave Earth and join them because they were aware of an impending doom to the planet. If this was in reference to the Celestial Host who battled Galactus in New York Harbor, or some other menace remains unrevealed.
Polaris' activities over the next three years and three months is unknown, however at some point she, Corsair, and Havok were made aware of the wedding of King Britain and Medusa and returned to Earth to attend the wedding. They had a reunion of sorts with other surviving members of the X-Men which was abruptly ended when Mr. S realized that the Sean Cassidy at the reception was an impostor (secretly Mephisto).
She is currently a crew member aboard (presumably) the Starjammer.