At some point, for an unknown reason, Doctor Doom launched it into space. His plan failed as the building is back in New York.
It appears in "The Man Who Stole Tomorrow" when Ant/Giant Man, Wasp and Thor escorted recaptured Blizzard to the Baxter Building where the portal to the Negative Zone is guarded by elite Mandroids.
In the The Private War of Doctor Doom, Iron Man and Wasp visited the building before it was attacked by Doombots. When the Skrulls invaded, the building was pulled across space before the Invisible Woman manged to reach her team and return it to New York.