In the middle of a world-wide kaiju attack by the Kilaaks, the Moonlight SY-3 was launched to find the aliens' base and mind-control transmitter on the moon. Landing on the moon's Cassini Crater, an Exploration Car was deployed from the SY-3, driven by several scientists and soldiers. When the device was discovered, the ground erupted into flames as the aliens mounted a defensive attack from their base against the humans. The Exploration Car drove across the lunar landscape, and fired its missiles at the base's entrance, destroying it. Now, the SY-3 returned to the air, and flew towards the transmitter, attacking it with all of its weaponry, but the missiles and bullets shot at the transmitter did little damage. Then, an idea was thought of. Taking one of the lasers from the Exploration Car, the SY-3 fired its new weapon at the transmitter, causing it to fall to the ground, and freeing Earth's monsters from their alien controllers. Victorious, the SY-3 blasted off, and returned to Earth. The SY-3 arrived home as Rodan was being set on fire by the Fire Dragon. Even though all the monsters had taken down King Ghidorah collectively, the spacecraft was too fast for them to attack, so the SY-3 flew in to help, blasting the Fire Dragon with its lasers and destroying it.
- Capable of space travel.
- Can fire a variety of missiles
- Able to deploy an exploration car.
The Moonlight SY-3 appears as an ally in Godzilla: Monster of Monsters. Like the Super X, it flies along the top of the screen. Sometimes it may leave power-ups while firing at the enemies. Its colors are different based on which kaiju is being used by the player, being blue for Godzilla, and gold for Mothra.
The Moonlight SY-3 appears as a playable unit in Godzilla 2: War of the Monsters. It requires that three shipments of parts be sent from one base to another and then a few turns pass while it is being assembled, but it is the most powerful unit the player can control.