The man known as John Howlett senior, was a rich man at the end of the 19th century, probably most well known for being the father of James Howlett, aka Wolverine.
John got his fortune due to hard work and the inherited fortune of his father, Old Man Howlett. Although John was a good man and a loving father, the family life was not as good as could be. His first born son, John Howlett junior would have died under strange circumstances. This also had a huge impact on John's wife, Elizabeth Howlett whom would not often leave her own room, much less leave the mansion or talk to her son. This concerned John, he thought his young son James (Wolverine) needed a mother, he already was an ill and fragile boy. Thankfully his son made good friends with Rose and Dog, two kids whom also lived at the mansion. Although John had some good times with his son, and staff, disaster was not far behind. Although this is never explicitly said in the comics, it seemed that John's wife was having an affair with the groundskeeper, Thomas Logan whom has a striking resemblance to Wolverine as he appears today. It could very well be that James was not John's son, but that of Thomas Logan. This doesn't mean that John wasn't truly the father or Logan, since he raised and loved him.
At one night, groundskeeper Thomas and his son Dog went back into the mansion (after being thrown out of the property by John due to an argument) demanding money and Elizabeth to come with them. John tried to defend his family, but was shot dead by the two. Seeing his father getting killed triggered James' mutant power, his bone claws first came to the surface and he killed
Thomas Logan in a fist of rage. After the massacre that left John murdered, and his wife (James' mother) dead by suicide, John sr.'s father, Old Man Howlett, helped young James and long time friend Rose to flee the mansion, giving them money to leave. Old man Howlett thought James to be somehow, but unwillingly, part of the massacre and thus wanted him out. Years later, the Old Man lay on his deathbed and had a change of sight. He wanted to find his grandson back, in order to keep the family name going. He had Dog track James and Rose down to bring them home. This was however misinterpreted-ed by Dog, who sought to find and bring the pair back by whatever means.
Although John may not have been James' biological father, he was everything a good father could possibly be, and Wolverine thinks back on him with only good memories ever since he had his memories returned after M-Day.
Earth 4011 (Wolverine The End)
For More Information see: Wolverine: The End
In this reality John Jr. Howlett was not murdered. Instead he caught his mother kissing Thomas Logan and John Sr. was forced to turn his son over to the Old Man, who took him away. The Old Man takes John's son to a mental hospital, but is unclear if John Sr. knew where his son was being kept.