At least Mindy's chapter makes a little sense because it's shown in the movie that she got to SpongeBob and Patrick by carriage, implying that to be the case, but the other two have no relation to the movie (or even the overall plot) whatsoever. And finally, one chapter features a strike being orchestrated by invertebrates because they can't see a chiropractor, and the plot is essentially trying to make peace with them and the vertebrates.
One chapter completely omits the Trench and the monsters altogether and replaces them with the foggy abyssal plains, where the entire plot is focused on solving a mystery at a hotel in the middle of nowhere in order to obtain a key item and return it to a cave. One chapter is dedicated to Mindy escaping Neptune's castle so she can find SpongeBob and Patrick and warn them of Plankton's scheme.
In the game, the desert takes up two whole levels, and the plot is pretty much made out of whole cloth.