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Here we have the Bruce Wayne of the timeline before the New 52, meeting his father, Thomas Wayne, who’s from the Flashpoint Paradox universe. The Flashpoint Paradox was the last DC event in which The Flash (Barry Allen) went back in time to stop the murder of his mother. This caused the timeline to change and gave birth to the Flashpoint Universe where a lot of major changes occurred. One of which being that Bruce Wayne was the one who got shot and died in the alley, prompting his father Thomas Wayne to become that timeline’s Batman. To fix the problem he caused, the Flash went back in time again and stopped his previous self from saving his mother. This act then caused the birth of a new timeline, the New 52.
From – Convergence #2