The Bhagavad-Gita

After the Xilien attack, Shinji and company are attacked by a large winged Kaiju, which Carver named "Hokmuto,"  which is a species of "MUTO."  They pursue it to an uncharted island, where they find a huge Kaiju that Misao claims is connected to the Necro-Kaiju somehow.  The Kaiju, codenamed Vishnu, was thought to have been a heavily mutated Kaiju, possibly infected and radiated while still alive.  To uncover the secrets, Shinji has to go inside, where he encounters parasitic creatures called Mutos.  He uncovers the secrets, and gets back in the transport cage.  Ibuki, still determined to take Miki back home with him, waits for everyone to leave, then leaves Shinji trapped in the cave.  Azusa finds him and gets him out, and they escape another MUTO, much larger than the winged one and having extra legs as well as an egg sac.  They realize that this is a mated pair.

They find the others held hostage by the Regulator and his remaining Xiliens.  It's revealed that Ibuki made a deal with them; if he turned Shinji in to them, the Regulator would give him a ship to leave.  However, he reneges on the deal and prepares to kill them all, and a fight ensures.  Godzilla then appears to attack the Xilien forces, and so does the male MUTO (attracted by Godzilla's radiation), but then, Vishnu awakens and destroys all remaining Xilien forces, killing the Regulator in the process, and then devouring the male MUTO.  Anguirus, Rodan, & King Caesar appear to help, but Vishnu easily dwarfs Godzilla, and throws his parasites at him and eventually swallowing him.  Then Mothra arrives and takes on a new armored form, slicing Vishnu's stomach open.  Godzilla then uses his nuclear pulse, obliterating the Kaiju before leaving.  Shinji barely manages to escape being crushed by Vishnu's carcass, but Ibuki then furiously attacks him, intent on killing him and take Miki back.  Suddenly, Miki intervenes and knocks him out, and Carver cuffs him to a pole before they abandon him.

Godzilla then fights Anguirus, Rodan, & King Caesar and beats them but doesn't kill them.  Afterwards, the female MUTO returns and attacks the group, but during her fight with Godzilla, a Necro-Kaiju brutally attacks her, infecting her into a new Necro-Kaiju, and Godzilla destroys both.

Later, Shinji and Miki finally marry, and Azusa begins to feel that she and Carver should get together...

Kaiju/Mecha:
-Godzilla
-Anguirus
-Rodan
-King Caesar

-Blazing Guardian

-MUTO

-Vishnu

-Mothra Leo