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Megatron has possession of the Nemesis, and the Maximals need a last-minute miracle to stop him.
Megatron has raised the Nemesis from its watery grave and has begun a random attack on everything in sight, all the while quoting the Covenant of Primus. Optimus Primal and Tigerhawk attempt to fight it off, but their weapons don't even scratch the hull. Tigerhawk tells Primal to rally the Maximals and that he will remain to fight. On the Nemesis, Dinobot II is commenting that his spark has changed and feels complete. Aspects of the original Dinobot begin to emerge. He admires Tigerhawk's defense. Tigerhawk is able to damage power on several decks, limiting Megatron's offensive options to using the fusion cannon, which he uses to destroy Tigerhawk. Going to the Protohuman settlement, Megatron prepares to destroy it. Dinobot objects, asking where the honor is in such an act, but Megatron fires anyway, killing Inferno and Quickstrike in the process.
At Mount St. Hilary, the Maximals are preparing a last-ditch strategy—bring the Ark online and fight the Nemesis. However, the ship has been offline too long, and Rhinox and Blackarachnia are having trouble restoring power. The Nemesis arrives, but Tigerhawk's attack has depleted its energon reserves, and the fusion cannon requires time to recharge. Megatron activates its tractor beam, and Primal enters the Nemesis. He and Megatron duke it out, but the Predacon clearly has the advantage. On the Ark, the Maximals manage to get the engines on line, but they burn out almost instantly. Rattrap proclaims that they are all going to die, and for once, no one tells him to shut up.
However, Dinobot II, disapproving of Megatron's actions, sends a message to the Maximals of an Autobot shuttle stored in the Ark. Megatron orders Dinobot II to fire, but he refuses, stating that he has his honor. In a last bid to save them all, Rhinox pilots the shuttle on a collision course with the Nemesis' bridge, crashing through the viewport and going out the other side. Optimus urges Dinobot to save himself, but he remains with the ship, biding farewell to Primal. As the Nemesis crashlands into the horizon, Primal rejoins the Maximals.
Some time later, the Maximals, having repaired the shuttle and rigged a transwarp cell to it, leave Earth for Cybertron. Optimus, piloting the ship, declares that the Beast Wars are over, and memorializes the Maximals who fell during the war. Rattrap, however, is more happy to be going home and points out that they won't have to see Megatron 'til they get there, as the Predacon is tied to the hull of their shuttle. As the shuttle enters transwarp, the scene shifts to the Protohumans, who have built a village and are using parts of Inferno and Quickstrike in a ritual to celebrate their new leader - Waspinator.
In the ultimate act of karma, Waspinator declares that he is "happy at last."
(Numbers indicate order of appearance.)
"You have already read the Covenant of Primus?"
"Just the good parts."
- -Dinobot and Megatron activating MORE guns on the Nemesis.
"Now where was I... Ah, yes, mindless destruction! Good for the Spark, I always say..."
- -Megatron Just before re-activating the guns on the Nemesis.
"Well, come on, let's have it—the usual 'destiny and honor' speech."
- —Megatron gets decked by Optimus Primal
"'And there came a hero who said, 'Hurt not the earth, nor the trees, nor the seas, nor the very fabric of time.' But the hero would not prevail'".
"Finish the quote, Megatron. 'Nor would he surrender!'"
- —Megatron and Optimus Primal
Rhinox: "Blackarachnia, how is that capacitor coming?"
Blackarachnia: "I need a conduit cable to finish the connection...ah!"
Blackarachnia takes Rattrap's tail/sword.
Rattrap: "Hey! Ya emasculatin' fembot!"
Blackarachnia: [Severs the point on the sword; Silverbolt shudders.] "Yes! Main thrusters connected to Teletron I!"
Rattrap: "It's Teletraan!"
Blackarachnia: "Oh, whatever".
- —The Maximals prepare for liftoff, witness a castration, and then fanwank.
"No power, no weapons... huh. We're all gonna die."
- —Rattrap and Rhinox
"Whoa, an Autobot shuttle!"
"The history tracks never mentioned this."
"History is still being made. Let's move!"
- —Cheetor, Blackarachnia, and Rhinox
"What?! What possible reason could you have to disobey me?! I am your master! I am your creator!"
"And I...have my HONOR!"
- —Megatron and Dinobot II
"Waspinator happy at last..."
- -Waspinator in charge of the protohuman tribe.
- On the Maximal side, this episode marks the death of Tigerhawk, and by extension, Tigertron, and Airazor.
- On the Predacon side this episode marks the deaths of Inferno, Quickstrike and the capture of Megatron.
- Dinobot II also dies, but which side he should be grouped with: kind of a toss-up.
- Optimus Primal's statement: "The beast wars are over, for now" foreshadow the events of Beast Machines.
- Kid Rhino's Season 3 box set contains an animatic with additional footage cut out from the final episode (presumably to save time, see Continuity errors.) One of the edits show Optimus Primal tearing out what appears to be either a Predacon power core (or a transwarp driver) from the Nemesis' control deck prior to telling Dinobot II to save himself. This device is later seen towards the end of the episode, installed to the controls of the Autobot shuttle as the Maximals prepare to return home, albeit very briefly.
- In the early plot of the episode, the Maximals successfully launched the Ark instead of an Autobot shuttle. Also, Dirge, Ramjet and Thrust would be reactivated and ram into the Nemesis instead of the Autobot shuttle. However, the ideas were canceled due to the show's limited budget and duration. This would have possibly explained where the three Coneheads came from when they suddenly appeared in season two of the original cartoon.
- It should be noted that had Megatron heeded Dinobot and not turned the fusion cannon on the proto-human colony, he would have most likely won the Beast Wars, by the simple fact that it would have been fully charged by the time the Nemesis reached the Ark (as pointed out by Dinobot, the fusion cannon's reactor was depleted to 70% power when they had arrived) without the Maximals having a chance to prepare in time. Also, he would not have killed Inferno and Quickstrike. Though normally the Predacons would have been able to recover from losing them, at this point the Predacons were very strapped for troops and supplies. In retrospect, this could be why he makes such a big deal about displaying honour later on.
- When the Nemesis' tractor beam is active, several items can be seen floating to the ceiling. These items range from Transformer related items (Rattrap's bombs, Rhinox's machineguns) to simply random real world items (telephone receiver, spinning tops).
- When crashing into the control room of Nemesis, the Autobot shuttle seems to take little if any damage.
Animation and/or technical glitches
- When Optimus cries "For pity's sake, Megatron; no more!" before first engaging in battle, Tigerhawk's 'shoulders' are flipped horizontally; wrong sides.
- As Tigerhawk is about to be overwhelmed by the fusion cannon, it cuts to a reaction shot by Dinobot, whose "monocle" is on the wrong eye.
- When Optimus returns to the Maximal base and tries to communicate with Tigerhawk, his right wing is missing.
- At one point, Optimus tears his wing off and tosses it to jam the giant grinder mechanisms on the bottom of the Nemesis. However, in the next scene in which he appears, his wing has been replaced with no explanation.
- As the Maximals await their doom inside the Ark and Rattrap comments on how they're "all gonna die", he's missing his robot-mode "backpack".
- Megatron apparently transforms to dragon mode off-screen, transforms back to robot mode on-screen before the scene cuts away, then when next we see him, he is in dragon mode again!
- When Optimus fires his chest cannons, the front parts of the cannons are at the back of them (attacked to the retracting mechanisms), and the blasts fire from the cannons despite the absence of actual barrels.
- For most of the episode, Optimus is missing the "blast shields" that he usually wears on either his forearms or shoulders.
- In the final battle scene, Dinobot is flipped horizontally. (See first glitch.)
- When Optimus reaches his base and the computer tells him that Tigerhawk has been destroyed, Rattrap's arm can be seen through the crack of the doors the whole time after Optimus bangs on them.
- Although it was cut from the final episode for time, the script called for G1 Megatron's spark to be removed from BW Megatron and placed back in its proper body before the Maximals leave Earth. This very brief scene was animated, and a clip of it can be seen on BWTF.com's page for the episode. The clip was also included on Kid Rhino's Beast Wars Season 3 box set. It should be noted, however, that despite the cut, Optimus' lines from that segment were still included in the episode, albeit used in a different context.
- Inferno can survive being completely vaporized yet can't survive being blown to scrap by the Nemesis. What?
- Keep in mind of the differences though. Just ONE huge shockwave verses a MASSIVE ONGOING BLAST OF PULSATING POWER... it's a little harder to survive such an onslaught.
- If Megatron haden't wasted troops by sending Inferno, Quickstrike, and Waspinator to find a new base then not only would Inferno and Quickstrike not be killed but Megatron may have won. They could've provided some good back-up for the Predacons during the fight, caught Dinobot as he was sending the blueprints of the shuttle to the Maximals, or even seen Rhinox flying the shuttle towards the Nemesis and shot it down. Then again it also makes you question why Inferno and Quickstrike didn't just call Megatron over their comms and tell him they were in the settlement.
- There is the Nemesis itself.
- "In the darkest hour, there will be a light," a line from the Covenant of Primus most likely derived from "Light our darkest hour" in The Transformers: The Movie.
- Megatron's line "Duly noted, Dinobot...AND IGNORED!" mirrors the original Megatron's line to Soundwave in the G1 series episode Masquerade.
- The lines Megatron reads from the Covenant of Primus bear some similarities to lines from English translations of The Bible of Earth's humans.
- One of such a lines: And you will know my name is Megatron when I lay my vengeance upon you. is derived from Ezekiel 25:17, a famous Bible passage which one of the film Pulp Fiction characters, Jules, recites every time he's about to kill someone. Just after reciting this Megatron launches attack towards Optimus and Tigerhawk.
- It's worth noting that the first part (before "Megatron") is similar to the first versions of passage, while the second (after "Megatron") — to the second, which ends with "you" instead of "thee", but maybe makers changed it because kids might have not know the archaic word "thee".
- BWTF.com page for "Nemesis Part 2", which includes a cut clip from that episode showing the restoration of G1 Megatron's spark.