Nautilus Prime is a mini-boss guarding the first Pet you can collect - Nautilus. The area where Nautilus Prime can be located is only accessible once Naija has the Bind Song. Having the Energy Form is also strongly recommended - whilst, in theory, it might be possible to defeat this enemy using the Bind Song and a nearby rock, it will be very difficult.
Once Naija swims close enough, Nautilus Prime will start to attack. In addition to spinning around the area and causing damage on impact, Nautilus Prime will release swarms of Nautilus and fire barrages of projectiles at Naija. The protective shell also means it will not take any damage unless it is inflicted at the pink fleshy part of the Nautilus.
Defeating Nautilus Prime will grant Naija access to the nest where the baby Nautilus pet can be obtained.