The Commander implemented (and possibly planned) a ruse to lure Hiccup and Toothless in for capture. He had his crew of a Dragon Hunter ship lay motionless on deck as if dead or unconscious, pricking the Rider's curiosity to investigate. Once Toothless touched down on the ship, the Hunters sprang up and attacked with dragon root tipped arrows. Hiccup and Toothless managed to escape, but not before an arrow struck Toothless in the tail. The two were able to make it to a nearby island, where Hiccup tried to hide a very groggy Toothless. The Commander and the crew fanned out across the island and searched for them. Hiccup was only able to elude capture because Dagur the Deranged was also stranded on the very same island, and had a change of heart about his purpose and actions in the world.
Eventually the Commander did capture Hiccup and Toothless, along with Dagur, and threatened to brand Hiccup if he didn't tell him where Toothless was. Dagur escaped, retrieved a revitalized Toothless, and flew in to save the day. The Commander turned tail and ran into the island interior, where he encountered a Changewing. Not knowing how to handle the wild beast, the scene ends with the Changewing lunging in for a kill at the Commander.
The Commander looks just like almost all Dragon Hunter characters look — helmeted, bulbous nose, no beard, and a built upper body with meaty arms. He also has green eyes. He wears a greyish-green tunic with a small red vest, the standard metal and leather helmet with spikes down the center, and a kilt of grey-purple and red.