My take on the story is as follows:
Rich man went to America and whilst there bought a strip of land and an native woman/girl as his wife.
They had a son (tom Hardy) and I'm assuming at some point the wife died.
Rich man takes a new wife and has a daughter with her. I suspect that at some point James and sister fall in love and possibly have a child that is passed off as his father's and wife's child.
James was sent to cadets where his commander was the guy who is the current chairman of the east India company.
James excelled at everything but there was a turning point where he suddenly rebelled and went 'mad' killing his senior officers, burning ships etc. James hints that he was only repeating what he was taught by the chairman.
James then takes off to Africa where he spends around 12 years before coming back when he hears of his father's illness.
Upon arriving back he hears of the strip of land he has inherited, he knows this is where his mother came from. He also knows this piece of land holds the key to Vancouver which is the access route to china. He owns a very valuable piece of land and the east India company are trying to hoodwink him into selling it for very little. They are now going to try and kill him.
He suspects foul play in his father's death so has him exhumed and his stomach contents tested. He was right it was arsenic poisoning.
I think that's everything so far.