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Henry's wife Nora Allen was killed by an unknown individual, with the blame being wrongly placed upon him, leading to Henry being promptly jailed as a result. His son forensics scientist son Barry, however, would often visit Henry there, hoping to one day personally prove his father's innocence.
In the DC Comics universe, originally Henry Allen died from natural causes. However this was retconned in Flash: Rebirth when Professor Zoom travelled back in time to Barry's childhood and murdered Nora Allen to get revenge on the Flash. With the blame placed on Henry, he spent the rest of his life in prison where he eventually died.