Life of Pi

Life of Pi.
Dark and opaque subplot.
I am sure, many would prefer not to acknowledge the true story, even if they logically understand that it is the only story plausible.

 So what was the story, as in real chain of events?

Ofcourse the one Pi tells in the end in very few words, as the alternate explanation given by him to the Japanese insurance guys.
Clearly all what Pi narrates about the tiger, hyena and zebra was a lie - euphemisms to the true story.

The true story is that the cook killed the Japanese sailor and Pi's mother. Pi killed the sailor. Pi ate a rat and human flesh, and survived for 227 days in the ocean.
For surviving 227 days, there was no way Pi could have been choosy about what he wants to eat. He had no option but to opt for the custom of the sea - ie survival cannibalism. Pi was to ashamed to openly admit but this was the only way.
Btw Richard Parker was also the name of the sailor in the  1838 novel of Edgar Allan Poe, where Richard Parker suggests to his fellow sailors to use one of them as food for others to survive. They draw lots and Parker gets canibalized in that novel. Btw a real life Richard Parker got cannibalized in 1884, and the name has come to remain closely associated with cannibalism. 

Coming back to Life of Pi, Pi turned cannibal, in the story it was his alter ego ie Richard Parker that killed and ate humans. 
When Pi was on brink of starving to death, he comes across a floating island, that provides him everything that he needs to survive. The island is of the shape of a human. It was a euphemism for a floating corpse. Pi discovers that the corpse that he is eating is that of a cannibal.(he discovers a tooth inside that island ie body)and fears other cannibals near by. He leaves the body once he understands that the water in that island has turned acidic ie the body is decaying. He ties his holy thread as a mark of his respect/ last rites that he can do on the ocean for a body.

 In the hospital, after breaking down over grilling by the Japanese insurance guys who do not believe the tiger story, Pi breaks down and tells Japanese insurance guys- what do you want to hear - you already know it. (Appealing to their logical reasoning) and tells them the truth. Japanese guys find it too dark to report, they would rather report a cock and bull illogical story, rather than a uncomfortable truth.

 "'So tell me, since it makes no factual difference to you and you can't prove the question either way, which story do you prefer? Which is the better story, the story with animals or the story without animals?' Mr. Okamoto: 'That's an interesting question?' Mr. Chiba: 'The story with animals.' Mr. Okamoto: 'Yes. The story with animals is the better story.' Pi Patel: 'Thank you. And so it goes with God.'"
Both the investigators agree that the story with animals is better one. In short they have started believing in miracles. 
The question is essentially do you want to believe an uncomfortable truth Or A soothing lie. A story which narrates a miracle ie an act of God is a soothing lie.
In any case Miracles are a way of putting a garb of respectability on uncomfortable truths. (Virgin mother-?? Must be a miracle... Sita swallowed by earth... Hello...)
 so it goes with God.