Mario's world begins to change when he meets a clone of himself named SMG4, and the two work together to not only build Professor E. Gadd's newest invention, Jet Jaguar, but also face off against monsters that appear out of nowhere. With Kaiju overwhelming both kingdoms, Peach and Bowser form an alliance to defeat the menace, and SMG4 works with graduate student Goombella, to not only find out about the Kaiju, but if they're related to a new material called Archetype. As the two go deep into the mystery, the king begins to rise from the sea to New Donk City.
After the death of all her family except for one younger brother, Lena Ichikawa sacrifices having a normal life to find the secret to the birth of kaiju: unnatural monsters that defy the natural laws of evolution. She knows they come from the trenches in the ocean where tectonic plates collide, but before she is allowed to the forefront of kaiju research, she must first gain experience working at a lab in the Defense Force. That means assisting military operations and avoiding a flirty vice captain who seems to think she's there to amuse him. It doesn't help that her precious baby brother keeps trying to get himself killed fighting kaiju. With all these distractions, she may never get to the bottom of how kaiju catastrophes come to be.