Penguin Commandos were mind controlled foot soldiers of the Penguin.
The commandos were pets of Oswald Cobblepot that became pawns in his fight against Batman. The engineers in the Red Triangle Circus Gang were seen constructing this equipment in the Penguin's office while studying Batmobile blueprints, before he decided to run for mayor.
They had special mind-control helmets that the Penguin had placed on them in order to use them as suicide bombers, as they would would be launching missiles at buildings all around themselves.
Eventually they all converged at Gotham Plaza, but Batman jammed their control system so that they would not launch their ballistic missile payload. Alfred was able to redirect them back to the abandoned zoo from a computer console in the Batcave. After Batman arrived and landed his Batskiboat on top of Cobblepot's fleeing vehicle, he tricked Penguin into using a hand-held signal device that caused the Penguins to fire their rockets in the zoo. It also released a swarm of bats from the skiboat that caused Penguin to step backwards into the Arctic World skylight where he fell to his death. As Batman rushed after him, he looked back the large structures being destroyed by the penguins behind him before zip-lining down into the exhibit interior. It's likely some of the penguins died amidst the chaos.
Behind the Scenes
The penguins that were used in Batman Returns were Blackfeet and King Penguins. Costumed actors portrayed the Emperor Penguins. Stan Winston's studio built many robotic penguins for the finale of the movie. This concept was likely inspired The Penguin on Parole story from Batman #38, in which he strapped explosives to living penguins. There are numerous other stories where Cobbplepot use exploding robot penguins to destroy his enemies.