The final battle rages between the Autobots and Decepticons aboard the Nemesis as the Omega Lock prepares to fire on Earth. Arcee questions if they should destroy the Lock should they be unable to capture it, but Optimus refuses, declaring he won't sacrifice a second chance to revive Cybertron. Ratchet arrives at the Lock and faces off with Shockwave, prepared to sacrifice himself to save humanity. Arcee is sent with Bumblebee and Smokescreen to back up Ratchet, while the Wreckers are ordered to take the bridge. Megatron enters the fray with the Dark Star Saber, and Smokescreen heads for the Decepticons' vault to grab the Star Saber for Optimus.
The Wreckers arrive on the bridge, but are quickly ground bridged away by Soundwave. Jack rallies Raf and Miko to help him face off with Soundwave, which works marvelously when Raf opens a ground bridge at the same time as Soundwave, trapping the Decepticon in the Shadowzone. Having secured the bridge, Jack tries to buy the Autobots time by taking the Nemesis on a joyride, but the Omega Lock is activated nonetheless. Optimus, whose jetpack has been damaged by Megatron, faces off with his nemesis on the Lock, while Arcee, Bumblebee, Smokescreen, Starscream, and Shockwave grapple over the Star Saber. Bumblebee manages to break free of the fighting and tries to leap down to deliver the Saber to Optimus, but Megatron kills him with several gruesome blasts of his fusion canon. Bumblebee's corpse plummets into the Lock, enraging Optimus, who furiously begins tearing Megatron a new one. Before he can finish him off, Megatron is able to retaliate with the Dark Star Saber, knocking Optimus to the edge of the lock. However, before he can kill his foe, Megatron turns around to an unfamiliar voice calling his name... only to have the Star Saber impaled in his chest by Bumblebee, restored by the cyber matter within the Lock. While everyone looks on in awe, Megatron dies, plummeting from the ship to the Earth. Starscream tries to avenge his master, but Shockwave drags him away to fight another day (though the ride in an escape pod is extremely uncomfortable).
Optimus announces Megatron's death to the rest of the team, and takes command of the Nemesis. Ratchet says that he never learned Shockwave's half of the synthetic Energon formula, meaning this may be all the cyber matter they may ever have. With Cybertron being a larger planet than Earth, Optimus orders the cyber matter prepared for Earth to be fired directly into the Well of All Sparks at Primus himself. The Nemesis bridges to Cybertron and finally revives the planet, restoring it to a healthy, glowing blue. Knock Out, who tried to flee the final battle, nonchalantly attempts to join the Autobots, but gets whacked by Miko for his troubles. Predaking, having clung to the ship the entire battle, flies off into the new dawn with intentions unknown.
On Earth, Optimus gives his obligatory speech with their departure to repair Cybertron imminent. Raf worries about the Decepticons still at large, but Fowler dubs the kids as agents - er, consultants, according to June - of Unit: E, who will help keep Earth safe with the Autobots departing. Ratchet steps up, declaring his intent to stay on Earth and provide Autobot aid to Unit: E. The kids tearfully bid farewell to their Autobot partners, and Magnus, Smokescreen and Wheeljack salute Fowler for all his help. As the team departs to Cybertron, Optimus shares a last, warm farewell to his best friend Ratchet, and takes one last look at his family on Earth as he finally goes home.
- Berserk Button: Optimus when Bumblebee is shot dead. Thankfully, he gets better.
- Big Damn Heroes / Back from the Dead: Bumblebee gets the biggest one in Transformers Prime history. Not only did the Omega Lock restore him, but he used the opportunity to finish off Megatron by impaling him with the Star Saber, saving Optimus Prime and finally ending Megatron's reign of terror.
- Big "NO!": Optimus, after Bumblebee's "death". Smokescreen appeared to do the same but his voice was muted at the time.
- Bond One-Liner: Bumblebee gets one when he terminates Megatron.
- Bumblebee: "You took my voice. You will never rob anyone of anything ever again."
- Book-Ends: Soundwave's first fight in the series was with Jack, Miko, and Raf. Guess who his final bout is with?
- Character Development:
- Early on, Smokescreen sees Megatron rising out of a hatch to join the battle, and stares at him for a second before rushing off to fetch the Star Saber.
- Ratchet deciding to stay on Earth. Remember, he was the most eager to return to Cybertron two seasons ago.
- Starscream's rage when Bumblebee kills Megatron, proving that, despite his actions earlier in the series, his newfound loyalty was genuine after all.
- The Comically Serious: Shockwave, sharing an escape pod with Starscream, who's whining about the lack of space.
- Shockwave: Do you intend to whine for the duration of the voyage?
- Dirty Coward: Again, Knock Out, who disappears for most of the episode before showing up on the bridge after Cyberton is restored, trying to change sides, but ends up pummeled by Miko.
- Disney Death: Bumblebee get blasted in the chest by Megatron, falling into the Omega Lock as his eyes fade out. Luckily, he is restored to life by the Cybermatter (with a repaired voicebox, to boot), and emerges just in time to save Optimus from Megatron. Predaking also survived being shot out of an airlock in the previous episode by hanging on to the Nemesis the entire time. He bears witness to Cybertron's rebirth before taking wing again.
- Earn Your Happy Ending:
- After three seasons, the Autobots finally manage to restore Cybertron!
- It's a bit of a Bittersweet Ending as well, though, since they have to leave their human friends behind. Though, as Bumblebee points out, they can Space Bridge back and forth at will.
- Eyelights Out:
- Megatron's eyes stop glowing just before he falls from the Nemesis.
- Bumblebee's eyes flicker out during his Disney Death.
- Exact Words:
- Ratchet: (to Shockwave) I cannot allow you to harm Earth.Shockwave: The planet will not be harmed, only its indigenous life forms.
- Forbidden Chekhov's Gun: The kids used groundbridge cross-streaming, which was accidentally done all the way back in "Shadowzone", to send Soundwave into the Shadowzone. May also double as a Godzilla Threshold.
- I Fight for the Strongest Side: This is Knock Out's reason why he wants to join the Autobots.
- Knock Out: What? I'm joining the winning team!
- HeelFace Door-Slam: Knock Out tries to join the Autobots - Apex Armor Miko punches him in the face.
- "Hell, Yes!" Moment: "Megatron is no more!" Cue the Wreckers cheering, Raf rendered speechless, Fowler cheering after a moment of quiet triumph, and Ultra Magnus smiling like he's been born again.
- Hoist by His Own Petard:
- Megatron ordered Shockwave to ready the Omega Lock to fire, allowing the cybermatter within to heal Bumblebee when he fell within after being shot by Megatron, who then proceeded to terminate the Decepticon leader.
- If Megatron had killed Bumblebee when he sadistically tore out the scout's voice box and left him for dead, he might have won.
- Soundwave is trapped in the Shadowzone by Raf, Miko and Jack, who managed to use his own Weaponized Teleportation against him.
- Impaled with Extreme Prejudice: Bumblebee runs Megatron through with the Star Saber.
- Killed Off for Real: Megatron... or not
- Meaningful Echo: "Until we meet again, old friend."
- No-Holds-Barred Beatdown: Optimus continually attacks Megatron punch after punch when Bumblebee is shot down.
- Rule of Symbolism: The light fades from the Decepticon insignia on Megatron's chest as he dies, signaling that with his death, the Decepticon cause dies as well.
- Screw This, I'm Outta Here!:
- After Megatron dies, Starscream of all bots initially wants to stay and avenge him, but Shockwave grabs him and runs off.
- As the Nemesis is being stormed by the Autobots, the first instinct that comes to Knock-Out is pack up and head for the hills. However, his escape attempt is hampered by crossfires on every corner, leaving him trapped on the warship, now under the control of the Autobots. He attempts to join the Autobots as a result of this, but gets punched in the face by Miko.
- Shout-Out: When Jack tells Raf to open the groundbridge to stop Soundwave, he refers to it as "crossing the streams", a reference to Ghostbusters (1984). May count as Celebrity Paradox, considering who voices Agent Fowler.
- Suddenly Voiced: Bumblebee.
- Took a Level in Badass: Working together, all three kids manage to trap Soundwave with his own Weaponized Teleportation!
- Weaponized Teleportation: Soundwave, as usual, though it ends up being his downfall.
- Wham Line: "Megatron! You took my voice. You will never rob anyone, of anything, ever again."
- Optimus Prime to Ratchet: Until we meet again, old friend.