Long before the big team-up in the Goo Caverns, there was battle against Cane and the Anti-Dino Machine. After considerable build-up, Cane finally got his hands on this giant Spider Tank and went on rampage, and it took the combined forces of Dino Attack Team, Alpha Team, the LEGOLAND military, and the two airships Saber and Voltage to finally take him down.
Alpha Team, Agents Defense Organization, Dino Attack Team, and Evil Ogel joining forces to battle Dr. Inferno and Mutant Dinosaurs in the Goo Caverns? Awesome. It's a shame that it no longer exists.
The Brickster blowing up the Dino Island Laboratory. While the RPG until that point had largely downplayed the Brickster's role in favor of Ogel and Sam Sinister, this classic LEGO villain finally got his moment to shine and show what he was truly capable of.
Somehow, Dust's death managed to be a Moment Of Awesome, a Tear Jerker, and a Moment of Heartwarming all at once, which can likely be attributed to that guy from that show's excellent writing of the character, build-up, and payoff.
After years and years of constantly falling into traps, Lord Sam Sinister finally learns his lesson and rejects Baron Typhonus's proposal.