Thomas knows that WICKED can't be trusted, but they say the time for lies is over, that they've collected all they can from the Trials and now must rely on the Gladers, with full memories restored, to help them with their ultimate mission. To complete the blueprint for the cure to the Flare.
What Wicked doesn't know is that something's happened that no Trial or Variable could have foreseen. Thomas has remembered far more than they think. And he knows that he can't believe a word of what WICKED says.
The time for lies is over. But the truth is more dangerous than Thomas could ever imagine.