Down but not out, Megatron discovers Tarantulas's secret tunnel network that leads to the Decepticon warship, the Nemesis.
The Maximals, secure for the first time since they moved into Mount St. Hilary, begin searching for the Predacons, who have been vulnerable since Tigerhawk destroyed the Predacon base. Optimus Primal quotes a verse from the Covenant of Primus, believing Tigerhawk's arrival to be divine prophecy.
Meanwhile, the Predacons are growing disaffected with Megatron. (Even Waspinator is mouthing off.) Inferno, ever loyal to his "queen", declares that a new "colony" will resecure them. Megatron orders him to take Waspinator and Quickstrike, while he, Rampage, and Dinobot 2 search the remains of Tarantulas's lair. Dinobot finds a hatch which leads to an underwater tunnel, which in turn leads to something that greatly excites Megatron.
Silverbolt and Depth Charge spot Inferno, Waspinator, and Quickstrike leaving. Optimus orders them to fall back, but Depth Charge heads in. Optimus leaves with Blackarachnia, Cheetor, and Tigerhawk to support them. As Primal arrives, Depth Charge finds the hatch—and a bomb. The explosion fails to kill any of the Maximals, but Silverbolt is damaged, and Blackarachnia and Cheetor escort his parts back to base.
At the protohumans' cave dwellings, Inferno declares that the caves will be their new "colony". He orders Quickstrike and Waspinator to engage, but Waspinator angrily refuses. Something had finally snapped in Waspy's central processor, and he declares that he is out of the Beast Wars. After a tirade against Megatron, the Predacons, life in general, and always being blown up, Waspinator tells them that they can kiss his stinger. Inferno and Quickstrike blast him, and proceed to attack the protohumans (who have become much tougher, having learned from the example of Dinobot and the Maximals).
In the tunnels, Primal, Tigerhawk, and Depth Charge continue searching. After locating a data terminal, Primal accesses it and discovers what Tarantulas found and Megatron desires—the Nemesis, the flagship of the Decepticon fleet and the vessel which shot down the Ark. Realizing the threat the Decepticon warship holds, Depth Charge heads out to locate it. Meanwhile, Megatron and Dinobot find that Tarantulas modified the vessel with a transwarp cell, installed a Predacon control console, and left behind a Covenant of Primus to boot. Megatron and Dinobot begin powering up the vessel for an attack.
Reaching the sunken behemoth, Depth Charge engages Rampage. The two enemies fight, and Depth Charge grabs an energon crystal. He drives it into Rampage's spark, and the explosion destroys both Transformers and also causes Dinobot 2 to cry out in pain. Optimus, though mourning Depth Charge's loss, is relieved to know the threat of the Nemesis has been dealt with.
That is, until the Nemesis rises from the ocean, fully operational. To be continued...
(Numbers indicate order of appearance.)
"Ant-Bot not find own thorax with both hands and a road map."
- —Waspinator gets in a decent dig in for once. Inferno drops him on his head for this.
[Silverbolt has been injured in an explosion]
Silverbolt: "Worry not, my love. It's just a...scratch."
[Silverbolt's arm falls off]
Optimus: "Maybe. But I think you're due some time in the CR chamber."
Silverbolt: "Sir, I'll be fine. I—"
Blackarachnia: "Shut up and obey your commander, bone-brain."
[Silverbolt's head falls off]
Silverbolt: "Yes, dear."
- —Silverbolt is pretty whipped.
"I said no! Dragon-Bot command you, Sub-Commander Kiss-Butt! Dragon-Bot not command Waspinator! Not any more! Waspinator sick of being evil. Sick of being Predacon! And Waspinator especially sick of getting blown to scrap all the time! Sooo, Waspinator quit! Hm! As of now, which means Ant-Bot and Two-Head can just pucker their mandibles and plant big, wet, juicy one right here on Waspinator's big...fat...stripy..." BAM!!!
- —Waspinator finally stands up for himself...and gets blown to scrap by Inferno and Quickstrike.
"You have to stop Megatron! At any cost."
- —Optimus Primal telling Depth Charge what must be done.
"Oh, it is more than that, my malevolent minion. That is the most powerful Decepticon warship in Transformer history. The ship that shot down the Ark itself! THE NEMESIS! The Nemesis..."
- —Dinobot II compels Megatron to give his most dramatic exposition...in this episode.
"I was your assignment, and you failed."
- —Rampage's last words.
"Raw energon! Right through your twisted spark! Take it! Take it straight to the pit, you SICKENING PIECE OF SLAG!"
- —Depth Charge's final words before killing Rampage.
- The death of Rampage is the only time in the series that a Maximal kills a Predacon (not for lack of trying).
- Waspinator officially calls it quits in this episode, but not before he gets slagged yet again.
- "Nemesis" was originally going to be a three-part episode, but was later compressed to two. 
- Apparently Cheetor can fly in his Transmetal 2 form. What, did he suddenly discovered that moving at Mach 2 can let him get airborne?
- Depth Charge is also seen flying in both humanoid mode and beast mode as well in a scene. Apparently this episode took many liberties regarding character abilities.
- At the beginning of the episode, when Rattrap holds up the Covenant of Primus, the Maximal variant of Cybertronix text can be seen. It reads "7 613 were cast out with him a cork one fork and a bowl of beans between them". This presumably follows the portion of the Covenant read by Primal, Datatrack 7.613: "And a mighty warrior came down from the sky, and a rainbow was upon his head, and his feet as pillars of fire. And the great dragon was cast out onto the earth, and his followers were cast out with him."
- When Megatron powers up the Nemesis, external ship lights illuminate Cybertonix text in the Predacon variant. It reads "red dwarf".
- This is the first time where Waspinator (who always gets blasted and speaks in the 3rd person) refers to himself as I. However, he calls himself by I in Season 1 "Dark Designs", but since he was knocked on the head and thinks he's Shrapnel, it doesn't really count, does it?
- Megatron orders both Rampage and Dinobot into the submersible with him. However, only he and Dinobot enter the submersible with Rampage following suit. Guess some people just like leg room.
- When Megatron is watching Depth Charge and Rampage battle from within the bridge of the Nemesis, he turns away to speak to Dinobot II and uses his dragon head to continue watching.
The Beast Wars retelling of the Ark's crash and the Nemesis differs from any previous version. In the original cartoon, the Decepticons used the Nemesis' tractor beam to lock into the Ark and it was the Autobot/Decepticon fight inside the Ark that caused it to crash. Microbots", The Nemisis crashed in an archeological site in the South America. ; in the Marvel comics, the Decepticons boarded the ship and Optimus deliberately crashed the Ark onto Earth , with the Nemesis being left abandoned (the UK comics had Galvatron destroy it ).Also, in "
As Beast Wars is intentionally not a direct continuation of any specific continuity, instead seeking to treat all previous Generation One stories as if they were Arthurian legend, this would imply that those accounts are not canonical in this series. Alternatively, Optimus could just have the details wrong.
Animation and/or technical glitches
- When Dinobot squeezes the piece of Rampage's spark he possesses to pacify his "half-brother", his shoulder pads are missing. Also, the spark seems to float freely when it is released, in contrast to previous episodes where it was held in place by Dinbot's spark chamber.
- At the very beginning when Optimus is reciting, in the background you can see Cheetor, in his normal Transmetal body, walking with Blackarachnia.
- In the Underground tunnel when Megatron figures out something, his wing went though his arm.
- When Megatron smacks Quickstrike for wanting to shoot at the Maximals as they try to hide, he uses his dragon tail. However, when the camera goes over to him, it looks as if he had used his humanoid mode right arm (or that he had not made any such motion at all) and his dragon tail does not appear to have moved from its stop behind his head.
- As the submersible prepares to depart, Megatron and Dinobot II look down the ramp and then at each other. At this time, Megatron's face is purple like his first Transmetal form.
- The flashbacks to the battle between the Ark and the Nemesis recounted by Optimus Primal and Megatron neglect to mention that the Decepticons boarded the Ark before the crash. This was probably done either to simplify the retelling, increase the significance of the Nemesis's involvement, or both.
- The bomb Megatron left behind as a trap for the Maximals has some very curious properties. It has enough power to severely damage Silverbolt and creates a powerful energy wave that is felt by the approaching Cheetor and Tigerhawk, who are miles away (even disintegrating a butterfly in the process). However, despite all of the above, Optimus and Depth Charge suffer absolutely no ill effects from the bomb, despite being at extremely close range and having very little time (or even room, given the terrain) to run for cover. This may, however, simply be because of the properties of Transmetal bodies, which Silverbolt is only part or being the heroic charecter he is jumped on the bomb inorder to save his Commander and comrade.
- Strangely enough, it also looks like a cartoon human bomb (several sticks of TNT strapped together, as opposed to some sort of technological futuristic Transformer explosive).
- How exactly did Megatron construct a bomb from scratch to begin with? With his base destroyed in the previous episode, it seems very unlikely that he would have the materials to create one on hand.
- Megatron refers to Tarantulas as Unicron's spawn. While from the context this appears to have been a generic insult (equivalent to "bastard" or "son of a bitch"), convention-exclusive fiction like Primeval Dawn have depicted Tarantulas as a literal creation of Unicron.
- This is the first source to give the Decepticon vessel that attacked the Ark a name.
- Optimus Primal tells Depth Charge to stop Megatron "at any cost," which echoes Optimus Prime's line, "...no matter the cost" in the Transformers movie during the Decepticon siege of Autobot City on Earth.
- When Dinobot II cries out in pain after the death of Rampage, brief flashes of the original Dinobot's animation model can be seen as he looks upward. This possibly alludes to the plot of the unproduced episode "Dark Glass", where Rattrap uploads the original Dinobot's datatrax into the clone. For more information on that controversy, please refer to these articles.
- Inferno calls Rampage a drone at least once in this episode. It is unknown whether the writers knew that a drone is a male ant whose main purpose is to mate with the queen, who in this case would be Megatron. Ewwww!
- When contacting the Maximals, Optimus encodes transmission "M Sipher", a reference to Greg Sepelak.
- Silverbolt's remark "'Tis but a scratch" followed by the dismemberment of his arm could be a reference to the immortal line of the Black Knight in Monty Python and the Holy Grail. Coincidently, the Black Knight is able to survive fatal mutilation. As well, you see a squirt of red fluid which looks very much like the Black Knight's blood after having his arms chopped off.
- Inferno utilizes the classic cartoon method of hiding, appearing from behind an impossibly skinny tree.
- The scene where one of the vertical stabilizers of Nemesis rises from the water and covers the sun is somehow similar to the scene from James Cameron's The Abyss, where the alien colony (coincidentally, known as the "Ark" in the script) surfaces and one of its "towers" does exactly the same —rises and blockss the sun.