In Cloudy With a Chance of Meatballs, there is a running plot line about the mother of protagonist Flint Lockwood. She believed in him, where his father did not.
It is mentioned in passing, that she died 12 years before the time in which the film is set, but not what actually happened.
How did Flint's mother die? Has it been explained?
As her wikia page explains:
Ten years prior to the creation of the FLDSMDFR she died of unknown causes and her death affected both Flint and Tim heavily. After her death Tim proved to have difficulties raising his son due to not knowing how to properly show him the encouragement his mother used to show him, however Flint would continue to be encouraged by the words she spoke to him in his youth throughout his inventing carrier.
In the end credits, her ghost is seen haunting Patrick Patrickson.
So no, it isn't explained in the movie.
However, it is possible we might learn more in the upcoming television series. Here's what Wikipedia says about it:
On October 9, 2014, DHX Media announced that it will develop and produce a television series based on the film franchise, titled Cloudy with a Chance of Meatballs: The Series. The series will be traditionally animated and will consist of 26 22-minute episodes. It will take place before the first film, showing Flint Lockwood as a high school student who dreams to become a serious scientist. In his adventures, he will be joined by Sam Sparks, a new girl in town and the school's "wannabe" reporter, along with Flint's dad Tim, Steve the Monkey, Manny as the head of the school's audiovisual club, Earl as a school gym teacher, Brent as a baby wear model, and mayor Shelbourne.
His mother died of unknown causes. When she died, it caused Flint's dad to have depression, and it is not explained in the movie.
