To put it mildly, Big Sir mauled Barry, smashing and pummeling him beyond recognition. The only upside was that the Flash was able to dismantle the armor Duncan Ratchet had been given by the Rogues, thereby returning him to his innocent state.
Then he collapsed. Thanks to his increased metabolism, Barry was always capable of bouncing back from injuries quickly, and this was no exception, but his face didn't heal properly. This was later to have a bonus in that his lawyer Peter Farley would later convince him to unmask during the trial, so that his secret identity was safe from exposure, but the psychological effect was worse.
The sequence of events that had begun with preventive measures against his worst enemy had spiraled completely out of control. Barry could no longer trust or depend on anything. His moral character alone had kept him going, actively pursuing the role of superhero even in the midst of the buildup to the trial...but even Barry was only human.
Finally, enough was enough. He stopped running. For the first time since he had been granted his super speed, Barry Allen slowed to the pace of an ordinary man, permanently. He didn't just slow down, though, he found that he had actually lost the will to live.
If it hadn't been for the remarkable coincidence of finding Farley, who had himself been the victim of physical violence at the hands of the Rogues, perched at the same bridge he'd chosen, the one that linked Central and Keystone City, the one he had once crossed to meet his idol, Jay Garrick, the original Flash...Barry would have done the unthinkable.
But Farley had been there, too. Ironically, the last time attorney and client met before the trial was when they had both been driven to the brink of despair. As all the Flashes have learned over the years, it's far easier to embrace destiny when there are others who understand what that means.
Together, they chose life.