This is the plot to season 2.
Part 1/3 of Season 2 A.K.A Vortaak Invasion Arc
The aliens known as the Vortaak come to Earth peacefully and begin to study the monsters. Koshiro and the others try to find a way to discover the aliens true intentions. When they discover the Vortaak's true reason for coming to Earth being to enslave humans and destroy all monsters they launch a full scale war assault on the aliens. All of the monsters that were even villains join in to save the earth. The Vortaak unleash several monsters and plan to obliterate the monsters swiftly. Koshiro, and Zack become the last 2 remaining of their group as all of the others are captured and their G-Modules are shut down. The Vortaak send down MechaGodzilla to destroy Koshiro as Luna states "If Koshiro gets captured or *gulp* dies then we have no hope of stopping these aliens". Koshiro and Zack team up as Godzilla and Orga and take down MechaGodzilla. They then manage to get into the alien ship and save their friends but Claire is captured as they all escape.
End of part 1/3
Part 2/3 of Season 2 A.K.A Energy Absorbtion Arc
The Vortaak unleash many weak monsters such as Ebirah,and The Giant Condor. They seemed to be linked up to some wireless energy absorbtion machine. When Godzilla attacked them they managed to absorb his attacks and needed to be destroyed by other monsters. Claire aboard the Vortaak mothership was forced to become Mothra and studied by Gigan. He is revealed to be able to do tasks he would never be able to do with the help of his human disguise. Gigan and Monster X are sent down to Earth to learn the human customs. They do this while waiting for Monster X to be fully charged with the energy of Godzilla by the monsters hooked up to the energy absorbing devices. Gigan is called to attack Godzilla this time. When he attacks Godzilla, Godzilla is cautious about attacking with melee moves due to Gigan's hooked claws and Chest Buzzsaw. Orga appeared and took down Gigan with ease. Gigan then transforms into something called a G-Form (Based on final wars appearence of Gigan) and kills Orga who after becoming Zack is grabbed by Godzilla and run to the scientist groups base as Gigan gives chase. Godzilla constantly tries hitting Gigan with atomic breath to slow him down but Gigan keeps absorbing the attack. Destoroyah flies in and hits Gigan with his horn katana. Megaguirus then flies in and copies Gigan laser eye beam and uses it on him. Godzilla manages to get Zack to the base and goes back to attack Gigan. Godzilla grabs the device on Gigan absorbing Godzilla's atomic breath, tears it off, destroys it, and obliterates Gigan's head with an atomic breath blast. All of the energy needed to complete Monster X's structure is obtained after Gigan is brought back onto the Mothership and repaired to go back to studying Mothra. Monster X is unleashed and attacks Godzilla with no power held back and almost obliterates him. But the monstrous Monster X soon begins to mutate due to the G-Cell power in the Godzilla energy in him and becomes.....
End of Part 2/3