Somewhat long and complicated, anyone who can make anything of this is a GOD.
An Autobot scouting party is captured by the Decepticons and locked up in the brig. Rather than interrogate them right away, instead the Autobots are separated into individual cells before being taken out one at a time. Each one is returned in a timely fashion - they started timing how long one was absent on the second day - but on the fourth day Cliffjumper is not returned to his cell. The remaining Autobots worry that the minibot got mouthy with the interrogator and was either offlined or has been sent to the repair bay. A few more days pass and finally one of the 'bots agrees to talk if the 'cons will tell him what happened to Cliffjumper.
Once the information has been obtained, the interrogator abruptly turns to the blacked-out observation window and asks if the Autobot is telling the truth. The window goes clear to reveal that the Decepticon command team and Cliffjumper have been observing the session, and Cliffjumper confirms that the mech is being truthful. Megatron orders the Autobot's memory files to be altered so that he believes that Cliffjumper is offline.
It turns out, even though the Autobots will never know (unless someone notices that the deal-making Autobot has altered memory files), that Cliffjumper has been a Decepticon from the very beginning, joining the Autobots as a deep-cover spy. He constantly threw around accusations against other, loyal Autobots to maintain his own cover. Because who would believe that the mech who sees a traitor around every corner is the one everyone should actually be watching? There remains one deep-cover operative back on the Ark, however, so it isn't as if the information will dry up...
As an aside note, I kind of think that CJ was reformatted into his current frame style, and will obtain his previous build once the Autobots are traded back for whatever Megatron decides to ask for so that he can finally get some goddamned payback against the mechs he was stuck living among for way too long.
Also, for some reason (probably because
sanjuno and I continue to share a brain) I kind of think CJ has some pre-war connection with the seekers and pretty much takes his orders from them more directly than Megatron.