As the name states, Ghost Condor is a giant, robotic contraption resembling a snake. It is mostly green with gray spikes, orange stripes, a red jewel on its head, and dark-gray parts on the lower torso. It has lime green under its mouth. It has black eyes with blue eye lids and yellow teeth (it is always seen grining). It also has two green cone-shaped structures with small holes in the center of the flat face which can pop out spikes. The structures each have metallic grey underside and a yellow spike at the end.
After the Ghost Condor's defeat, Whisker runs away but leaves behind a tablet that is in another language. Marine offers to translate but Blaze steps in and translate, where the message described a floating landmass, much like Sky Babylon, that fell into the sea. Tails wonders about the landmass and what connection it could have to the pirates. If the player heads to Sky Babylon first, Blaze will suggest heading toward Blizzard Peaks.
The battle takes place on an endless road displayed on the Touch Screen which the player runs on, while the Ghost Condor constantly hovers above the player on the Top Screen. Unlike most of the game's 2.5D boss fights, the camera is here positioned behind the player, making the boss fight area a pseudo-3D stage, although the player retains normal horizontal movements and mid-air actions. At the beginning of the fight, there will be Ring clusters on the road to withstand the Ghost Condor's attacks. New Rings will not appear later on.
The Ghost Condor will first fire two types of mines from its tail. The first is a red, spiky mine that will damage the player on contact, so move away or Spin Jump/Axel Jump over them. The second is a green mine which the player will need to jump on to get propelled up to the Top Screen (like a Spring) to attack the Ghost Condor. When launched by the green mine, the player can perform Trick Actions, the Humming Top/Hop Jump and the Axel Tornado/Jump Step, but the Super Boost/Fire Boost is not available for use. Sometimes, the Ghost Condor may summon green fish-like robots, which when destroyed, will launch the player upwards like the green mines.
When reaching the Top Screen, the player can land on one of the Ghost Condor's floating cone structures and use them as platform to continue attacking the boss. Eventually, it will fire a homing missile at the player, so the player must jump back down to the Touch Screen to avoid it (all missiles fired will despawn at this point).
As the fight progresses, the stage scrolls faster. The Ghost Condor may sometimes drop down to the Touch Screen and spin towards the player; to avoid this, move to the far side of the road when it starts moving. It will also send one its floating structures to attack the player in a couple of ways:
- The structure appearing directly above the player and tracking their movements. This will also block any of the player's attempts to reach the Top Screen. Eventually, the structure will sprout spikes and slam down on the ground.
- The structure will hover at irregular heights on one side of the stage's road before sprouting spikes and moving to the other side of the road. The player needs to jump or stay on the ground to avoid this attack.
When the Ghost Condor's Boss Gauge is almost depleted, the Ghost Condor will drop down and drift helplessly sideways in mid-air until the player hits the jewel on its forehead to finish it off. If the player takes too long, it will regain some health and the fight will continue.
- Despite its name, it does not resemble a Condor, which is a name of a bird.
- When launched into the air by the green mines, fish-like minions or rebounding off the Ghost Condor, Sonic/Blaze can perform tricks but because the Super/Fire Boost can't be used in boss fights, the tricks apart from Hop Jump and Axel Tornado are merely useless in this case but with the two said tricks, it can help the player to stay up on the floating cone structures and continue hitting the Ghost Condor.