Ghost in the Machine

Not even fifteen seconds in and Starscream appears before Scourge and possesses his body, using him to fire blindly at the other Decepticons with mindless joy, prompting Galvatron to make one of his trademark snappy decisions and plan to blow up the traitor, though Cyclonus tells him that his comrade is merely malfunctioning. After watching Scourge bicker with himself, the emperor of destruction believes him to be a lost cause, but while his minion pleads for his life...
 

Galvatron is blasted straight in the chest, forcing him to hide behind rubble while Cyclonus, the Sweeps and the Predacons bombard their ally with laser fire, nailing him in the chest as well, but he escapes to the skies in his star ship form, Starscream explaining to his host that he intends to get his own body back, and Unicron is the only one who can give it to him.
 

The Decepticons check up on their leader, who simply demands that Scourge be captured and brought back to Chaar, with Cyclonus and the Sweeps sent for that task. However, they believe him to be switching alliances when they spy him heading towards Cybertron, and return to inform Galvatron, oblivious to the fact he is only heading for Unicron.

Inside Unicron, Scourge reactivates Unicron with surprising ease and immediately sets into demanding a body from him, though the remains of the mighty destroyer will only comply once three trials are completed; Scourge attempts to flee while Starscream hears this, but the Seeker reminds him that Galvatron wants him dead, so he has no choice but to assist him in the first task: Swiping Metroplex's optics.
 

Kup and Spike arrive at Autobot City to inspect the premises and how well things are doing, but while Kup is rambling on about Blaster doing a good job in security, Starscream attempts to possess the elderly Autobot, only for an explosion to knock them both away and completely disable Metroplex's security! The crew are dispatched immediately, with a rather large Bumblebee finding the thief...

And tripping him up, causing the eye to shatter before making an exit into Metroplex's voice chamber. A minor setback, as the Decepticon intruder merely takes the other one, sets a time bomb inside and makes a quick exit with the Aerialbots, Powerglide and Warpath on his trail, while Metroplex awakens and starts stumbling around helplessly and firing his lasers everywhere in a feeble attempt to find his eyes.

After zapping Powerglide and having his eye sockets explode, the people inside manage to get him working again afterwards, but are left to inform Rodimus of the bad news. Starscream directs Scourge to a cliff near Trypticon, explaining that since one of the eyes was lost, one that belongs to the Decepticon city will surely make a good substitute. Runabout and Runamuck are left to defend the city, so Scourge appears before them and stands in his defence, explaining his apparent betrayal was actually part of a secret mission for his leader.

Starscream uses this opportunity to possess Runabout and blast Runamuck in the face, and takes out the former by running him into a wall. The two thieves sneak in and swipe an eye, but Runamuck activates the alarm, sending Astrotrain, Thrust and Dirge out on the hunt for them. Scourge trips up Astrotrain and Starscream possesses him for the advantage of his larger cargo space, and they set off, loading both eyes in and making an easy escape.

While Galvatron berates his useless lackeys, Scourge delivers the eyes to Unicron while Starscream leaves Astrotrain to the Autobots, abandoning him above Cybertron and letting him get shot down by the Protectobots. Unicron finds the eyes satisfactory, and sets them about their second task: To bring Trypticon to him.

Meanwhile, Rodimus disses Astrotrain when interrogating him, and Blurr alerts them to Unicron getting his eyes back, allowing Rodimus to finally realise what's been going on now with the two Decepticons. Sky Lynx drops Ultra Magnus, Springer and the Protectobots over to Unicron, where they find the lack of Starscream and Scourge to be rather suspicious, only for the latter of them to show up and start blasting away.
 

Sky Lynx leads him away, only for Unicron to awaken and stun the Autobots inside him with an electric force and jettison them outside, their transport taking them back to Cybertron to rally reinforcements, while Scourge is forced to stay under the reprimand of having his body taken away from him by the one who supplied it to him.

Galvatron attempts to execute his failure-providing lackeys, who simply flee and hide inside Trypticon, who suddenly transforms without authorisation, Starscream being the one behind it and attempting to squish Galvatron before taking off into space, the Decepticons following after. Rodimus Prime, meanwhile, provides a completely unnecessary explanation of what just happened.

Starscream brings Trypticon to Unicron, only to be told that his current task is not yet complete until the transformation cog is removed and installed within his head; however, the Decepticons arrive and start blasting away, leaving Scourge to do that task while Trypticon is used to hold them off. This sight is pretty puzzling to the Autobots, though after a Sweep and Divebomb are destroyed, Galvatron commands a retreat. This leaves them with only the third task to perform, and it's a doozy!

Unicron demands they connect his head to Cybertron to act as his body.

Scourge wants none of this and beats feet back to his buddies to inform them of what Unicron plans to do, though Trypticon disabled their weapons so they can't help much. Scourge then informs the Autobots of the same thing, who also can't attack directly, but they can strike from within Cybertron when the connection is made.

Runabout, Runamuck, Thrust and Dirge are still inside Trypticon, who has now moved Unicron into range of Cybertron, and use this opportunity to start smashing things to prevent Starscream from controlling the robotic reptile anymore, and somehow succeed! With no physical body in his control, Starscream demands that a body be crafted for him so he can finish the job, and Unicron complies...

Only for Starscream to reply "do it yourself!" when told to finish the connection, much to nobody's surprise. However, both he and Unicron are rocketed into space by energon explosives planted at Unicron's roots by Ultra Magnus and crew, meaning Cybertron is saved!

Starscream, meanwhile, spirals through space and passes right by Galvatron, who commands his troops to blast his treacherous former comrade (even though he just said they were disabled only two minutes ago). Cyclonus, however, finds it peculiar how that Starscream is tumbling through space, an activity that ghosts can't physically do, unaware of him being a physical being now despite the fact he's clearly smoking from where Galvatron blasted him as the jet drifts into the vast darkness of space.

Rodimus, as thanks for informing them of Unicron's dastardly scheme, allows Scourge and Astrotrain to go free, and applauds Ultra Magnus on a job well done overall. However, he does need someone to retrieve Metroplex's eyes from Unicron, which is a task no one stands up to, so he laughs and claims he was joking, suggesting they'll just build new ones what with the energon explosions probably damaging them beyond repair. Everyone laughs and Unicron's eyes gleam. Spooky!

Even though all but his head was completely destroyed, all it takes is two wires fused together to get Unicron operational again.

Yes, that's two Ultra Magnuses in that last image.

Divebomb quite clearly explodes when Trypticon fires upon him (and completely understandable, guy's fighting a frigging dinosaur city), he's in mint condition when Starscream floats by later on. Then again, Dirge apparently exploded in both the movie and the last part of The Five Faces of Darkness, so I guess the Decepticons are gifted with both flight and damn good at rebuilding themselves.

For whatever reason, each special team featured in this episode only has two of it's members at a time. First it's Razorclaw and Headstrong, then Warpath and Bumblebee, two of those Aerialbots I never remember, Warpath and Powerglide, Dirge and Thrust, and Hot Spot and Groove. The only team to have all of their members together is the Battlechargers, with Runamuck and Runabout. Nutty!

Wheelie and Arcee each appear once at the screen in the episode, but have no other appearances or input. I'm a pathetic person for noticing. And I suppose mentioning that you never hear if Powerglide is repaired or not would just be ridiculous nitpicking for a throwaway scene.