Rodimus taking on an entire Decepticon base, all by himself in issue 13. And almost getting away without a scratch
And Megatron's effortless take down of Rodimus is a Crowning Moment of Awesome for the villains as he sends Rodimus hurtling out of the base and into space with just one blast of his weapon.
In the International Incident Arc. Vortex proves his badass Credentials. When the autobots show up and start fighting the combaticons, He gets shot up, and throw into a confusion through a smokescreen. Whirl pulls off a rotor (It's a sword, who knew), slashes Cliffjumper, dispells the smoke, and gets up into the air, taking on Jetfire, cutting off his wing, and sending him flying into Broadside (taking both out for the next few issues). He even pulls his boss out when they retreat.
In issue 17, Optimus Prime meets the newly reformatted Megatron and Soundwave, holding Ultra Magnus prisonner. As Megatron boasts about how invincible he has become, Optimus simply shoots Soundwave in the head, much to Megatron's fury.
And from the issue right after that where Optimus hits Megatron WITH A SATTELLITE.
And then he goes to lecture the entire Senate, fighting his way through their entire security forces, while carrying Whirl on his back. He's still trying to lecture them even as their goons are trying to throw him out. And in doing so he makes himself too much of a public figure for the Senate to simply murder in the night.
The Unnamed Senator gets a bit of mention as well, for saving Orion from the Senate's wrath, along with having him repaired and rebuilt with a compartment for the Matrix.
Megatron's hypothetical three questions he had for the Senate, long before he turned to violence, which Orion repeats. They are; In whose interests do you exercise power? To whom are you accountable? And how do we get rid of you?!
Sandra, a woman who betrayed Skywatch and the Autobots to the world because they had violated several laws, and had breached so many ethical clauses, gets captured. Pennington gives her the rundown, about how they are a unit, and she betrayed them. She counters that they were breaking an order from the president himself. Pennington gives her the speech that they are a unit and that the president never fought with them, Semper Fi, and all, and they should do illegal things, because they are a band of brothers. When he leaves, Ultra Magnus tells her that he agrees with what she did, she followed protocol, and stopped the people from breaking the law. It's such a swerve on genre, showing that it is not okay to run off half cocked, even if you have good intentions.
Megatron versus the D-Void, which has assimilated nearly every other Decepticon and made them fuse into one gigantic monster. He ignores it completely, and fights it one on one.
Cyclonus breaking free of Galvatron's brainwashing and immediately attacking him for everything he made him do.