During the final battle against 'M, after Anom tricks 'M into absorbing him, 'M's anti-legendary shield is destroyed. This is followed by almost every single legendary Pokémon (including Arceus himself) showing up to take down 'M once and for all.
Ghetsis has brainwashed Kyurem, and DS and Wolf attempt to use the Grey orb to bring Kyurem to its senses. Ghetsis orders Kyurem to freeze everyone to death, and DS proceeds to move even closer to Kyurem, despite the fact that it is already charging up the attack and she could possibly freeze to death by standing so close to it if Kyurem didn't return to its senses. With Wolf's help, DS manages to bring Kyurem to its senses and save everyone.
After nearly five years of parental neglect, Herbert decides to Call The Old Man Out and tears into Titan, following a series of chess metaphors and a Shadow Aura illusion on Psyche's part.
Ren's escape from being kidnapped and held hostage by Cipher. After be tortured by Aelia and Odin and having Kitsune threatened by Mammor: Mammor's Evil Gloating finally causes Ren to snap. In a state of Tranquil Fury, Ren busts out Cipher Operations HQ on Citadark Isle. Highlights include rendering a Peon unconscious with The Blade Of Kusanagi, using Trick Room abuse to stave off a squad of armed Peons, and ruining Mammor's left leg as payback for being responsible for Ren's left leg being ruined.
Vierr defeating Verax all by himself.
Paula's Humiliation Conga during the Special Acquisitions raid, culminating in her getting marooned in a PMD-A desert as a Corphish by Grace.
Every, along with the members of his team which can fly, battle and very nearly defeats a Latios. Starts here.
During Cipher's invasion of Gateon Port, Crewe holds off a large group of Peons on the main road with the help of her slingshot, Clockwise, Beedrill, and later Trixie and Lockspur (Hunter's Golduck and Roserade). This culminates in the four Pokemon (and Crewe, who occasionally attacks with her slingshot) facing down a Shadow Garchomp, Shadow Hydreigon, and Shadow Metagross all at once, and Clockwise facing off against a Shadow Goodra on his own, before the peons all eventually flee. The final battle with the pseudos is here.
Tangent and Xatu summoning a whole bunch of the J-Team's old friends and allies in order to help fight Cipher at Gateon Port during the Orre arc climax.
Jacob gets two after Cipher's collapse. The first is after Zeal's RedEyes!Aspect takes control and goes to try taking control of time with Jirachi, the battle moving into his Mindscape part way through. The second is two days after, Jacob challenging Titan to a battle tipped horribly in Titan's favor, where he manages to make a major turnabout of the battle, successfully snag Regina, and proceeds to finish it off by defeating Titan's Infernape, Omega, with Sylva.
Crewe fighting off Esprit after he tries to possess Straw for his ability to repeatedly cheat death.
Bishop the Scizor beating down the Malamar who had enthralled Kirk for nearly a year, as well as many other mons.
All of the Constantin vs Tagg battles, starting from here, here, and here respectively.
Though it's more of a villainous CMOA than a heroic one,( and it's a bit too horrifying to be a straight CMOA) the Wolf tearing through the Fairy Queen's masses and then the Queen herself definitely counts as being seriously badass.
Dune, after months of attempts, makes it to the top of Mt. Battle and not only defeats each of the last ten trainers with minimal injuries, he takes down Mt. Battle Master Battlus... before being challenged by the Heatran of Mt. Battle. The same one that was Shadowed back in the Cipher arc. Using a combination of Rill the Mega Swampert and Anja the Lilligant, Dune manages to fight the Legendary to a standstill and wins when both Rill and Grandpa Mountain collapse from exhaustion... but Anja, having hid behind the Mega Swampert in fear, never went down, earning Dune the victory.