Dr. Magnus Honey was Jennifer Honey's father and Agatha Trunchbull's brother-in-law and adoptive grandfather of Matilda Wormwood. He was killed by Agatha Trunchbull but it was ruled as suicide by police, due to there being no other explanation.
He worked as a doctor and was married to Mrs. Honey, who died a few years after the birth of his daughter Jennifer. Magnus asked his wife's sister (step-sister in the movie) Agatha Trunchbull to come to stay with them and help him look after his daughter and the house. Magnus loved his daughter greatly but he did not know that Trunchbull was being abusive to her whenever he was out of the house.
Some time after Trunchbull moved in, Magnus died. The police came to the conclusion that he killed himself because they had no evidence that anything else could have happened. The novel does not give any more information about how he died. In the movie, he is seen lying over his desk, dead, before his body is then carried away on a covered stretcher to a police car. Trunchbull made a fake version of his will to ensure she would inherit his property (the will is not mentioned in the film).
It is strongly implied that Agatha Trunchbull murdered him, possibly just because she wanted his property. When she sees a message on the blackboard that appears to be written by the ghost of Magnus (but actually by Matilda Wormwood using her telekinetic powers) it ends with a threat that "I will get you like you got me." Trunchbull is terrified when she sees the message. Fearing this 'ghost' will take revenge on her, she returns everything she stole from Jennifer and moves away.
In the film, Magnus would give his daughter the nickname of "bumblebee." Jennifer later revealed to Matilda a memory of Magnus giving half a big piece of chocolate to her from his chocolate box. After his death the box of chocolates would be counted by Miss Trunchbull so Miss Honey couldn't even sneak one.
In the musical, Magnus is a circus performer who gave Jenny a scarf belonging to his late wife. His murder is implied to be caused by a gun due to a banging sound and red lights when Matilda has a vision of his death.