Unlike most other Godzilla games of the era, Super Godzilla is not a pure action game. Instead, the player must guide the famed monster into the different levels by pressing the adequate button in the appropriate place. The game is split in two screens: the top one shows the actions Godzilla is making at the moment, while the bottom one shows his location on the current level. When Godzilla finds a monster to battle, the game switches into a standard side-view fighting segment. This game is famous for featuring Bagan, a monster that was considered for multiple scrapped films but never made an appearance outside of video games, and Super Godzilla, a more powerful form of Godzilla that influenced the design of SpaceGodzilla.
Invading aliens have now approached Earth, threatening all life. The fate of the world lies in the hands in a small group of people, who enlist the aid of Godzilla. Controlling the monster through a transmitter on the Super X2, players must lead Godzilla through several cities, taking him to fight a final boss that awaits at the end of each level. Aliens and monsters aren't Godzilla's only worries, as he will face smaller obstacles such as tanks, electricity towers, mines, and UFOs as well.
As the game goes on, Godzilla fights and defeats all of the aliens' monsters. After defeating their final monster, Bagan, he returns to the ocean. The human characters note that even though Godzilla saved the human race this time, he may yet return to threaten them in the future.
- The player can use a wide variety of items to help beat enemy monsters.
- Godzilla can smash through mountains, buildings and towers, but this causes damage.
- Beat the Mother Ship and you will eliminate all the UFOs for that round of the game.
- Each level is timed, and if it is not completed in that time the player will fail the level.
- The player can only hold four colored orbs at a time, which can only be used in battle mode.
- The terrain that the player walk on will affect the speed of which Godzilla moves (deep water takes a great deal of time to wade through).
- Godzilla - Defender of Japan, the monster that once destroyed civilization became humanity's only hope for survival. In his quest to rid the Earth of its aggressors, Godzilla was aided by a small band of humans that controlled the King of the Monsters as he faced the horrors beyond a thousand stars.
- Super Godzilla - After King Ghidorah was resurrected as Mecha-King Ghidorah, the human characters determined that Godzilla must increase in power, and so Godzilla had to seek out the three capsules of Super S energy, only then would the reptilian creature transform into the godly stature of Super Godzilla. After defeating Mecha-King Ghidorah, Bagan, the ultimate enemy monster of the game appeared and Godzilla again changed into Super Godzilla in order to combat him.
- King Ghidorah - The boss of the first stage. King Ghidorah attacks by either firing one, two, or three of his gravity bolts. The more he uses the more damage the attack does. Being the first boss of the game, King Ghidorah is viewed as the easiest. His attacks are very weak, and he has less health then Godzilla.
- Mechagodzilla - The boss of the second stage. In the American version, the Showa Mechagodzilla (initially disguised as a Fake Godzilla that only takes one hit to defeat) is fought, while in the Japanese version, the Heisei Mechagodzilla is fought instead. Both versions are mostly the same, the only difference being that the Heisei Mechagodzilla uses a mouth laser instead of finger missiles (its laser does more damage) and can fire rockets from its shoulders, and the Showa Mechagodzilla's triple slam attack does sightly more damage than the Heisei Mechagodzilla's. Both versions have an eye-beam attack. The Showa Mechagodzilla has a force field attack that will block Godzilla's standard atomic breath attack, which will be followed by a large missile firing out of his chest. The Heisei Mechagodzilla, however, will absorb Godzilla's atomic breath and reflect it back (which is odd as in the film, Mechagodzilla uses its Plasma Grenade after absorbing Godzilla's atomic breath). A strong atomic breath attack will pierce Mechagodzilla's shield and cause considerable damage. Mechagodzilla's attacks aren't particularly strong compared to later bosses and its health is slightly less then King Ghidorah's, but it can be hard to hit because it often slams into Godzilla. Even though Mechagodzilla only the second boss in the game, it's viewed as an extremely hard battle.
- Biollante - The boss of the the third stage. Initially Biollante has vines that will keep Godzilla from attacking her. Biollante attacks with her vine tentacles and a spray of acid (her most damaging attack). Biollante will not be damaged by Godzilla's body slam, and using it will cause her to counter with one of her own, which does less damage than the acid spray but more than the vine attack.
- Battra (also referred to as "Battle Mothra" in the U.S. game manual) - The boss of the fourth stage. Battra can only be hit by Godzilla's more powerful atomic breath attack. Fortunately, Battra only requires about five hits to kill. It will either attack by ramming Godzilla or by firing its prism beams (the dive bomb does more damage). After Battra is defeated, another one will appear in an undeveloped state in the stage. If the player is quick enough, he or she will be able to reach and defeat it without a battle. If not, they will have to fight another Battra, which is identical to the first one except it has a little less health.
- Mecha-King Ghidorah - The boss of the fifth stage. Mecha-King Ghidorah is essentially a far more powerful and much more difficult version of King Ghidorah from the first stage, with the same attacks, which inflict far more damage, and has far more health, the second highest amount of health next to Bagan. Mecha-King Ghidorah has one additional attack, tasers, which are his most powerful attack. Mecha-King Ghidorah is viewed as a extremely hard fight if fought normally. However, the player has the option of becoming Super Godzilla before the battle, which makes the fight one of the easier ones in the game. Mecha-King Ghidorah's attacks inflict considerably less damage to Super Godzilla, who has more health Mecha-King Ghidorah. Super Godzilla's attack will also inflict far more damage than Godzilla, capable of draining one-fourth of Mecha-King Ghidorah's health in one hit.
- Bagan - The final boss. Bagan initially appears as a floating energy pod that obliterates Tokyo and is chased by Godzilla throughout the final stage. Once Godzilla reaches the end of the stage, Bagan transforms into his final form and the boss battle is initiated. If the player chose to fight Mecha-King Ghidorah as Super Godzilla, then Godzilla will start this battle as normal Godzilla. Bagan is generally seen as impossible to defeat as normal Godzilla since Godzilla's attacks will hardly inflict any damage (while Bagan has the most health of any monster in the game), and many do no damage, while Bagan's attacks (in order of weakest to strongest, a claw slash, a barrage of white diamond like stars, and white plasma beam) do more damage than any other monsters. As Super Godzilla, Bagan is still viewed as a hard, but beatable opponent, since Super Godzilla and Bagan have the same health and their attacks inflict roughly the same damage.
While praise was given to the story and graphics, Super Godzilla did not get very positive reviews. A common complaint among players is that the computer is given unfair advantages; it can make decisions much faster than an average player ever could, and will oftentimes spam attacks. Additionally, if the player gets three game overs, he or she will have to start from the very beginning with no way to try again, as the game lacks a password system.
- Super Godzilla's physical appearance is the direct inspiration for SpaceGodzilla, and the space monster's physical form is an almost direct duplication of Super Godzilla's appearance from the game with only minor, mostly cosmetic changes.
- The Japanese version of the game features the MechaGodzilla from the then recent film Godzilla vs. Mechagodzilla II. Since the film had not yet been released in the United States, the American version of the game features the Showa Mechagodzilla instead.