For most of the novel, there isn't much good to say about Dr. Thomas Stone, other than that he's a dang fine surgeon. But things do get a little more complicated than that, and here's what you need to know about deadbeat-dad-turned-liver-transplant-pioneer.
Dr. Stone was born in India to English parents when it was still a British colony. (More on that chapter of history here.) Stone grows up mostly on his own, due to his mother's fatal illness and his father's fatal alcoholism. Because he has spent so much time in the hospital with his dying mom, he just naturally falls into medicine and becomes a kick-butt surgeon.
His claim to fame, at least while he's in Ethiopia, is the fact that once he had accidentally cut himself while working on an infected patient—which means that he had just exposed himself to some nasty germs. When he saw that he was infected, too, "He made a quick decision: to amputate his own finger before the infection spread farther, and to do the operation himself" (1.2.6). Yeah, he totally amputated his own finger. Can you imagine?
What's more, his missing finger makes it even easier for him to "negotiate crevices and tissue planes that others could not, and his middle finger had developed the dexterity of an index finger. That, together with the fact that his middle finger was longer than his former index finger, meant he could tease an appendix out from its hiding place behind a cecum (the beginning of the large bowel) better than any surgeon alive" (1.2.8).
In this way, Dr. Stone's weakness becomes an advantage. But some of his other weaknesses take a little longer for him to overcome.
Yeah, it's too bad Stone's toughness doesn't extend to dealing with life changes that don't involve chopping off limbs. When he realizes that the nun he loves has just given birth to his sons and died in labor, he doesn't respond as you might expect a guy who can calmly amputate his own finger would. Nope. He runs for it. While Hema, who will later adopt the boys, tries to remind him of his responsibility, Stone ducks out:
"You heard me, Stone you killed her," Hema said, raising her voice so that she drowned out every other sound. He flinched as the words lashed into him. It pleased her. She felt no pity. Not for a man who wouldn't claim his children. He pushed the swinging door so hard it shrieked in protest.
"Stone, you killed her," she shouted after him. "These are your children." (1.10.61-62)
And that's it. All we get of Stone is his back as he flees the hospital. Until a couple of decades later, that is…
When we finally meet Dr. Stone again, it's in New York, where he's picking up a liver for a transplant operation. Poor Marion is shocked to see his biological father, who's now a famous surgeon pioneering new liver techniques, and of course he has to hunt him down. Marion and Stone have a few rocky starts, but finally Stone explains that he used to have fever and alcoholic spells, and it was during one of those spells that he and Sister Mary conceived the boys.
Luckily, in an Ethiopian restaurant in New York, Dr. Stone finally says the words that he should have said so many years before: "'I'm so sorry,' Stone said. I don't know whether he was speaking to me, or Ghosh, or the universe. It wasn't enough, but it was about time" (4.47.75).
Stone finally uses the combination of his guilt and his surgical prowess to perform the liver transplant that saves Marion and kills Shiva. It's like he is both redeemed and punished all in one.