Thawne is referring to the Particle Accelerator. Barry, Cisco and I all got our powers from it. Eobard built a Particle Accelerator and Cisco and I worked on the project. Unlimited clean energy was the goal. Unfortunately, Eobard had built it to fail. His goal was to create metahumans, people with abilities. I discovered that the system was flawed and eventually realized it was designed to explode. That was when I was fired from the project.
Eobard is a time traveler who got stuck in our time. He wanted to go back to his own time, but he needed the Flash to do it. So he orchestrated Barry getting his powers, which had apparently been an accident in the original timeline, with a deliberate Particle Accelerator explosion. And, in the process, he ruined a great many lives.