According to Wiggo, Kennaugh attacked (he's been second three times in this race) and Thomas "stupidly" chased him down, then Brad rode over the top of them and TT'd to the finish. If they'd all come in together Thomas would have won easily.
When he crossed the line, Kennaugh did not look like he'd just colluded to throw the race, particularly after he only decided to compete on the Saturday morning.