Some boats have shark shields which hurts any sharks that enter them (although they can't outright physically stop a shark).
Scaly Petes first boat was reinforced with marine grade alluminum.
Scaly Pete says that a megalodon attacked a navy boat, and only 3 of its 16 crew survived.
The Atomic Leviathan shoots a big beam of energy into the sky once the shield around its encloser is taken down (by some clever moves from the Shark).
The Leviathan destroyed the thick concrete wall around its encloser.
A ship which is flickering in and out of existence can be seen below Plover Island (this is a reference to
the Philadelphia Experiment).
Humans can pick up and throw exploding canisters far.
An orca sends the Shark flying high into the air.
Human cloning is something that happens in the military.
An active underwater secret base can be found in the Gulf.
A vast unknown kaiju is bound behind a gate on the sea floor in the gulf. What looks like flames and (somehow) black smoke emerge from it sometimes, and whatever's trapped on the other side looks like it's trying to break its way through, and would be far bigger than not only the Shark, but even the Atomic Leviathan.