Mebius unlocking the power of Burning Brave mode and using it to defeat the Imperiser in Episode 30 "Flames of Promise".
In Episode 46 "Immortal Glozam", Ms. Misaki, Konomi, Marina, Dr. Fujisawa, and Dan Moroboshi rescuing Mebius from his frozen crucifixion by Glozam. Then, when Ultraseven and Ultraman Mebius reduce Glozam to just his head in the ensuing fight, Konomi and Marina activate the Bringer Fan METEOR, which has been modified to unleash superheated air, melting Glozam into nothingness before he can regenerate. Yup, GUYS just defeated one of the 4 Heavenly Kings. Now that's girl power.
The battle between Maquette Zetton and the combined strength of Mebius, Miclas, and Windam in Episode 27 "Champion of Fierce Fighting". Add that to the sounds of GUYS cheering Mebius on, and we have a battle that captures the spirit of determination and teamwork against unstoppable forces that embodies the Ultra Series.
The final battles against Alien Empera and Bogalmons in "Words from the Heart" and "Pride of GUYS" respectively.
Ultraman Mebius and GUYS destroying Birdon in Episode 3 "Only One Life". GUYS shoots Birdon's venom sacks/wattle, pumping the poison into Birdon's own body, and as the monster screeches in agony, they fire a force field METEOR around the monster at the exact moment Mebius shoots his Mebium Beam, containing the resulting explosion. GUYS just managed to defeat a monster that took three episodes to kill in its initial appearance with some damn fine teamwork and well-aimed shots.
Ultraman Mebius' battle against Gudon in Episode 2 "Our Wings". After trashing Tokyo in his battle against Dinozaur in the first episode, Mebius demonstrates how much he's learned by tossing Gudon away from the city.
Sayuri Hinode overcoming the Alien Serpent's control over her in Episode 30 "The Invincible Mother" with nothing but her sheer willpower to be reunited with her family.
Ultraman Leo and Mebius destroying Alien Reflect using their Leo Kick and Mebium Drill Kick to smash clean through his body.
The battle between Ultraman Hikari and Alien Babalou in Episode 35 "Azure Waves of Light and Shadow".