(Note: The Nemesis is never named in the original animated series nor in the Marvel comics, and was not named until Beast Wars.)
Marvel Comics continuity
(Note: Events from the UK Marvel Comics are identified with italics.)
Megatron and his crew of Decepticons used the Nemesis to chase Optimus Prime and his crew of Autobots out into deep space. Eventually, the Decepticons boarded the Ark, the Autobots' ship, and left the Nemesis orbiting Earth. The Ark then crashed into Earth with all the Transformers onboard, deactivating them and leaving the Nemesis in orbit with Shockwave to watch it.
The Nemesis remained undisturbed, hidden from Earthling view with superior cloaking technology. In 2006, Galvatron traveled back in time to the year 1986 in order to build a large laser cannon to destroy Unicron. Upon completing the cannon, Galvatron tested its effectiveness on the orbiting Nemesis, destroying the ship with a single blast.
During the Decepticon Civil War, Shockwave's base was the Nemesis, which he had parked at the bottom of the ocean 4 million years ago when he fought the Dinobots. (The ship's identity and part of its backstory was revealed in the letters page, which directly conflicts the earlier UK story. Simon Furman wrote both stories.)
Generation 1 animated continuity
In 1985, archaeologists eventually discovered the ruins of the Nemesis in South America. Once Soundwave relayed the news to Megatron, the Decepticons deployed immediately. Upon arriving, Megatron removed the Nemesis's power-source, the Heart of Cybertron and had Hook then install it in him. Imbued with near-limitless power, Megatron then attempted to destroy the Autobots, and almost succeeded, until the Heart of Cybertron was removed from his body and destroyed by Perceptor, Brawn and Bumblebee.
The Nemesis was the flagship of the Decepticon fleet, and the most powerful warship ever built.
According to myth, it was responsible for shooting down the Ark. It was revealed that Tarantulas had discovered the wreckage of the Nemesis deep under water, and had been refurbishing it for unknown purposes. Following Tarantulas' death, Megatron discovered the rebuilt ship and commandeered it as a last ditch attempt to rewrite history and destroy the Ark.
Using the Nemesis's awesome power, Megatron managed to kill Tigerhawk as well as Inferno and Quickstrike by accident. In the final battle, the Nemesis's controls were severely damaged by Rhinox and Optimus Primal. Out of control, the ship crashed a second time at an unseen location far over the horizon line.
Even for the flagship of the Decepticon space fleet, one might have considered the armament on the Nemesis to be overkill. In addition to the standard energy weapons used by the Decepticons, the vessel carried a massive amount of missiles, which could be fired slowly in a swarm of rocket propelled death. A tractor beam could pull anything beneath it up to be sliced and grounded up by rotating blades and drills. The blades were incredibly sharp, being able to slice through solid rock.
Given that Megatron himself would have be the ship's normal commander, it shoould not be surprising that the primary weapon on the Nemesis was a fusion cannon. The fusion cannon was powered by its own reactor, apparently separate from the main Energon supply. The reactor would require a powerup time between blasts.
Dreamwave comics continuity
After returning to Earth following Shockwave's defeat on Cybertron, Starscream used the Nemesis as his base of operations. It is unknown if the warship had previously been used for this purpose by the Decepticons or if Starscream rediscovered it after returning to Earth.
The technical specifications for the Nemesis were:
- Estimated length: 2.5 miles
- Wingspan: 1.75 miles
- Height: 1.25 miles