The 18-year-old Irish striker ripped rock-bottom Brighton apart in Johan Boskamp's last match as Stoke manager.
The big Dutchman, who is on his way back to Belgium after one season in charge at the Britannia Stadium, has lost patience with the club's owners for failing to resolve his future while a takeover bid by former chairman Peter Coates rumbles on.
He has left behind a real prospect in Rooney, 18 earlier this month. The Dubliner opened his account in the sixth minute, the Brighton defence allowing him time to pick his spot from close range as they appealed for offside.
Rooney doubled the lead midway through the first half, sidefooting home a cross from on-loan Australian Josip Skoko.
Stoke went further in front in the 40th minute, Darel Russell turned to strike a shot from 20 yards against the underside of the bar and, as the Brighton defence again failed clear, Mamady Sidibe turned past his former Gillingham team-mate Guy Butters to slide home for 4-0.
The misery continued for Brighton after the break. Skoko and Sidibe combined for Rooney's hat-trick, with a right-foot rasper from 12 yards from 63 minutes.
Paul Reid, Brighton's Aussie defender stumbled over to allow Stoke sub Peter Sweeney to stroke home the fifth with eight minutes left.
Brighton sub Doug Loft scored an 84th minute consolation, a left-foot drive into the bottom corner from 15 yards giving the former Gillingham youngster his first senior goal.
It's was Brighton's seventh successive defeat against Stoke and their heaviest at the Withdean Stadium.