Michael is the only one of his 4 sons, including Tom, who didn't die a violent death:
Tom Hagen's Death in The Godfather's Revenge
In 1963, shortly before the president's assassination, while on vacation with his family in Florida, Tom was doing some business for Michael at the Deauville Hotel in Miami, after meeting with Ben Tamarkin and Senator Patrick Geary. He left and was surprised by Nick Geraci who had been hiding in the back of Tom's car and secretly following him for days. He had Tom drive to a rural, swamp filled area and then knocked him unconscious with his pistol.
When he came to, he realized his hands and feet had been duct-taped together and his car was sinking into the swamp and quickly filling with thick, brown water. He then had a memory of meeting Sonny, and being taken in by the Corleone family and his wife Theresa and two sons and two daughters and dies with a happy memory in his head as the water engulfed Tom and the car totally. Though his body was never found, Michael Corleone was sent by Nick Geraci a dead baby alligator with Tom Hagen's wallet in its mouth, to imply that Tom Hagen slept with the alligators. He was 54 years old.