During Tom King's run, the heroes found out that Eobard Thawne had placed Thomas on Prime Earth so he had to watch his son live out the same brutal life as a vigilante that Thomas had.

Source: https://www.cbr.com/thomas-wayne-batman-before-flashpoint-dc-comics/

Feeling he lost too much, Flash traveled back in time to capture Eobard Thawne before he killed his mother, Nora Allen.

Source: https://www.cbr.com/flash-flashpoint-alternate-versions-dc-comics-tv-movies/

Tom's exciting portrayal of Eobard Thawne has been unforgettable for nine years and fans will be delighted to know that he's brought that same wonderful intensity to our finale, too."

Source: https://comicbook.com/dc/news/the-flash-tom-cavanagh-always-knew-series-finale-return-reverse-flash/