“You can’t trust them.”
– Orion

Since the Mauser incident, Chuck and Sarah haven’t exactly been trusting each other very much. Though Sarah’s cold-blooded kill wasn’t the catalyst for all the mistrust, it marked the beginning of a trend. Now, while the romantic feelings still linger, the trust is gone, and Orion’s words do nothing to bring it back.

If you haven’t already, make sure to read the disclaimer.

“Chuck Versus the Lethal Weapon” put our hero on a quest: find Orion, and get the Intersect removed. Chuck approaches this quest with a determination that we haven’t seen from him before. Nothing will stop him from doing what needs to be done. If he has to launch a covert web search operation, he’ll do it. If he has to misappropriate a computer held under lock and key by the United States government, he’ll do it. If he has to break the trust of the woman he loves, he’ll do it.

Vincent: “I wish I could give you a proper reward, but, unfortunately, I have to shoot you.”
Chuck: “It would be unprofessional not to.”

Chuck also has newfound confidence. He faces down Vincent (who has a remarkable ability to survive near-death situations) as if daring the enemy agent to attack. Luckily, Casey and Sarah manage to rescue Chuck in the nick of time. However, they’re too late to save Orion, who apparently blows himself up to stop Fulcrum from capturing him. Thus, the search for Orion is terminated.

For a few hours, Chuck believes that his quest has reached a dead end, and suddenly, the determination and confidence that he had gained are gone. But Orion didn’t leave Chuck with nothing; under his pillow, Chuck finds a CD-ROM with a final message from Orion, encouraging him and telling him that it’s possible to remove the Intersect from his head. Chuck also finds the Intersect’s schematics. It looks as if Chuck’s quest is far from over. But that means that he can’t fully trust Sarah yet; she works for the government, and the government wants to keep the Intersect in his head. So, he keeps the Intersect schematics to himself.

The episode’s powerful final scene shows Chuck alone on his bed, ostensibly reading a comic book, but actually using it to hide the schematics that he is perusing. He can keep it a secret for now, but as we know, all secrets are eventually revealed.