Meanwhile, there is an expedition to Adona Island in which a giant egg is uncovered, believed to be a remnant of prehistoric times. Shortly after the remarkable discovery, the expedition team is attacked by two pteranodons. The UN receives word of the two dinosaurs and dispatches Mechagodzilla to deal with them. The mech is successful, killing one of the pteranodons and sending the other collapsing into the nearby sea. The scientists then leave the island, egg in tow.

Upon the scientists return to Japan, the egg eventually hatches to reveal a newborn Godzillasaurus, as opposed to a pteranodon as speculated. The scientists then propose a hypothesis of how this came to be as a brief scene accompanies the discussion showing a pteranodon fighting a Godzillasaurus in prehistoric times. In light of the discovery, it's feared that Godzilla might try to rescue the infant. The fear is quickly justified as a report comes in that Godzilla is attacking an oil refinery, and making his way toward the laboratory. In response, the UN send Mechagodzilla to attack the nuclear menace. The two towering monsters battle it out until a mechanical failure occurs allowing Godzilla to defeat his robotic clone.

Godzilla continues onward to the lab; however, upon arriving Godzilla suddenly turns away, leaving the vicinity. It is later discovered that the Baby Godzilla can communicate telepathically, and was sending off distress waves which caused Godzilla to leave. The UN, seeing the tactical advantage that this presents, sets up a new plan to kill Godzilla in which the infant is used as bait. As an extra precaution, the UN also readies an older war machine, Garuda, for combat in order to ensure Godzilla's defeat at the hands of Mechagodzilla. In order to execute the plan, Baby Godzilla is sealed away in a canister so it can be shipped to a remote location. While in transit, the small Godzillasaurus sends out a distress call.

Meanwhile, in the shores off Adona Island, the pteranodon that was knocked into the sea awakes and, due to a heavy exposure to radiation from the local nuclear deposits, transforms into Rodan. Rodan then flies to Japan to answer Baby's distress call. The winged monster discovers the helicopter that is transporting the small Godzillasaurus, and quickly destroys it and carries Baby off to safety.

The UN reacts to this change of events by deploying Mechagodzilla and Garuda to finish off the pteranodon. Rodan tries his best to defend Baby Godzilla from the mechanical monster, but in the end is slayed. Shortly after Rodan is killed, Godzilla emerges from the nearby water. Mechagodzilla splits into two parts to attack the nuclear menace. Eventually Godzilla is killed, but not at the expense of Garuda being defeated. The flying war machine's nuclear reactor then explodes and the fallout from the detonation resurrects Godzilla who this time defeats Mechagodzilla once and for all. Godzilla then carries Baby Godzilla, with his teeth, out to sea.

The Mechagodzilla character was also vastly different in this early draft, as the robot was modeled more closely after the Showa version and was given the power to break into two separate war machines, a concept which would be used for Moguera in Godzilla vs. SpaceGodzilla (1994).

The final scene to this script was also changed, as Godzilla was originally going to carry off Baby with his teeth, an idea that was dropped because it was thought "that the scene would not be very convincing because Godzilla was so much larger than Baby Godzilla" - Wataru Mimura, writer.

The ending to this draft was also different compared with what would be seen in the final script. In this version, Godzilla is revived thanks to Garuda exploding, not Rodan's sacrifice, and this was likely changed in order to make Rodan a more respectably "third pillar" in the film next to Godzilla and Mechagodzilla. It should be noted, though, that this was not the next choice for the ending, as a revision later appeared which did not feature Godzilla being revived at all. However, his death triggers a reaction causing the fallen Godzilla to explode, resulting in Baby Godzilla rapidly growing to full size and attacking Mechagodzilla.