Sonic the Hedgehog and Tails flew to the Wing Fortress in their bi-plane to comandeer a shuttle so they could fly to the Death Egg. When they arrived, there was no sign of Robotnik and defenses were light, so it seemed to be abandoned. Venturing into the interior of the ship led Sonic to be trapped by the automatic weapons (actually the boss from the level). How or why the Wing Fortress remained airborne isn't explained at all.
The ship returned in the Issue 258 story, Sky Chase. Upon discovering secret plans in the Desolate Dust Zone, Sonic learned that the Wing Fortress was airborne once again and took off to bring it down. Once again, Tails took him to the flying ship and the hedgehog took down another "boss". This time, however, Robotnik had lured him into a trap. The madman planned to steer the collossal vehicle into the Metropolis Zone, killing everyone there and Sonic inside. Fortunately, Sonic was able to power up a Star Post onboard, creating a vortex large enough to suck the entire fortress inside. It reappeared inside one of Robotnik's factories, rendering the base completely unusable.
- The Wing Fortress is supposedly over 3000 metres long.
- Sonic left a Clucker Badnik to shoot at him once more, suggesting that there is no organic battery inside it.