Super Godzilla vs. Mecha-King Ghidorah
When reaching stage 5 of the game, the player is faced with a choice to face the resurrected King Ghidorah, via Mecha-King Ghidorah as Godzilla in his base form or as Super Godzilla. Requirements for Godzilla to change into Super Godzilla in this stage is to collect three special energy capsules marked "S". However, during this time, Mecha-King Ghidorah is causing mass destruction in Tokyo, and the research center that carries the Super Energy Bank that is another requirement for Godzilla's transformation will be on the verge of being wiped out if the destruction of Tokyo reaches 50%.
When fighting Mecha-King Ghidorah as Super Godzilla, the damage that Super Godzilla takes as oppose to the amount of damage Godzilla would take is reduced by more than half. Super Godzilla's attacks can inflict massive damage to Mecha-King Ghidorah, which means that Mecha-King Ghidorah can be defeated with minimal effort. It would be apparent at this point that Super Godzilla is superior to Mecha-King Ghidorah.
Super Godzilla vs. Bagan
In stage 6, if the destruction of Tokyo is less than 50% despite Mecha-King Ghidorah's attacks, than Godzilla can easily become Super Godzilla simply by obtaining the Super Energy Bank produced by the research center. If the destruction of Tokyo is more than 50%, then Super Energy Bank is non-existent and the second Super X will have to be used to collect the energy needed, however, the player must stall Bagan as Godzilla while this is happening.
Super Godzilla is widely regarded as a requirement to defeat Bagan as Godzilla in his base form can take high levels of damage from Bagan's attacks, and Godzilla's offensive attacks will do little to no damage to Bagan. Bagan is seen as a difficult opponent even when playing as Super Godzilla, but one of the most easiest tactics to use against Bagan is Super Godzilla's super punch (where the player charges the attack by holding the punch button and releases the attack by letting go of the button) to heavily stun Bagan in order to activate Super Godzilla's special attacks. Damage done to Super Godzilla by Bagan is reduced by more than half (just like with Mecha-King Ghidorah) and Super Godzilla's attacks can inflict far greater damage to Bagan than Godzilla's attacks. Both Super Godzilla and Bagan have the same amount of life points which shows that the two monsters are equal in strength.
As Super Godzilla, Godzilla's appearance changes. His skin tone changes to a dark purple from the original greenish gray, his chest and abdomen region is colored neon green, while below his chest, there is a rib cage pattern that holds his lower abdomen. Also below the chest, there is also a new "Core" that has the ability to control energy inside Super Godzilla's body and release it into a powerful blast of energy in the form of a beam with a Godzilla head in the front of the beam. Godzilla's size increases a short amount, as well as an increase in strength due to a growth in muscle mass with two massive spikes sprouting from his shoulders. In the Japanese version of the game, Super Godzilla also has a Crest, or Crown, on his head, as well as what appears to be claws above the Mandibles.
- Energy Tail - Energy is channeled into Super Godzilla's tail, and then it is launched toward the opponent. Unlike Godzilla's Tail Swipe, Super Godzilla does not slam its tail onto the target.
- Explosive Shoulder Ram - Super Godzilla rams into the opponent with broadened shoulders. The enemy then explodes temporarily.
- Nova Breath - Basically a powered-up version of the Atomic Breath. However, it is orangish-yellow in color, and it does a lot of damage.
- Navel Blast - Super Godzilla's most powerful attack. The Navel core shines as energy swirls around the tip of the navel. Finally, Super Godzilla unleashes a blast from its navel that swirls until the tip of the beam morphs into the head of Super Godzilla and continues to blaze through until it hits the opponent. This Attack Does Tons of Damage to Mecha-King Ghidorah, therefore a battle using only Navel Blasts is a fast way to finish the battle, as it doesn't take that much of a fighting spirit to use the Navel Blast.
All of Super Godzilla's attacks are more powerful than normal Godzilla's. He has more health than normal Godzilla and doesn't take damage from attacks from non-bosses. In addition, as Super Godzilla the damage that boss attacks do is roughly cut in half.
In the Game Gear game Godzilla: Giant Monster March, Super Godzilla has an attack called Spiral Fire.
- Super Godzilla inspired the appearance of SpaceGodzilla. The shoulder spikes have been replaced by two large crystals, the "crown" that appeared in the Japanese Super Godzilla can be seen on SpaceGodzilla, and the Navel Core has been removed.
- Super Godzilla also appears in the Game Gear game Godzilla: Giant Monster March.