Well, first of all there is the allegorical explanation for the mystery of the animals themselves. You can analyze each of the animals Pi ends up on the small boat with as a representation of a different character: so, the orangutan represents his mother, the hyena represents the chef, etc. Richard Parker is Pi - he represents the inner savage side of Pi that allows him to be able to do what it takes to survive. There is also the mystery of the little island, home of the cannibalistic trees. I like to think of this island as a test to Pi: his "savage," animalistic side (Richard Parker) would like to just stay on the island; it's easier for Pi to embrace this side of him here; he doesn't struggle as much with RP on this island. However, every night there is the risk he'll be literally swallowed up by the island, suggesting that the longer he allows his animalistic side to exist, the more it will consume him until he is swallowed up by it entirely. This is why he makes the choice to leave the island; he makes the choice, though, difficult, to continue the human struggle. The mystery of why he tells the story through allegory to begin with? It is an easier, more effective way to convey the truth of the situation.