McDonald, of course, partnered Verry Elleegant to a brilliant win in the 2021 Melbourne Cup.
Stormy Marco is not in her league, but he justified the faith of punters, who sent him out the $4.40 favourite, with the second win of his eight-start career.
Ridden conservatively early from barrier 14 in the 16-horse race, he was able to improve at every stage McDonald wanted to before being presented early in the straight.
He surged to the front at the 300m and dashed clear to score a two-length win over $101 shot Cold Shower with the first filly to contest the Derby in 36 years, Quick Finish ($21), 1-1/4 lengths away third.
"It's a funny thing barrier draws, we drew the car park, but when you're drawing inside you feel like you have to hold the spot," McDonald said.
"If this horse probably drew inside, we would have been niggling to the first corner, a little bit disorganized.
"I just want to keep it smooth, I wanted him to relax. I had Zahra (Mark, on Vallice) to my inside and he was saying, 'sleep baby, sleep'.
"That's all we did, the two of us, and he had superior form."
The win was McDonald's second Victoria Derby success, following victory three years ago on Riff Rocket, who was also trained by Waller.