You might have thought he was referring to the trigger-happy first officer, but no! After speaking so respectfully of Skaldak, he has decided that the best thing to do would be to chain up the Ice Warrior. And, boy, is he pissed when he wakes up! He's also pretty bummed about having overslept by several millennia.
"The Ice Warriors have a different creed," the Doctor explains to Clara and the Captain. "By his own standards, Skaldak is a hero." Because Wikipedia didn't exist in the 1980s, the Doctor also has to explain to them that the Ice Warriors became cyborgs to survive the freezing Martian cold. Officer Crabby doesn't believe them. "These people are clearly enemy agents," he says. "We don't even speak Russian," Clara says. As soon as she says it, she realizes she is speaking Russian, or that at least they're hearing her that way. The Doctor explains it's the TARDIS's translation matrix, which seems to be working even though the TARDIS is nowhere near them. The Captain dismisses Officer Crabby. (I'm writing that in Russian, by the way. The TARDIS is just translating it for you.) The Doctor is very quietly angry. "All we needed to do was let Skaldak go, and he would have forgotten all about us." Well, then, chaining him up was probably the wrong move, right? "But you attacked him, you declared war." He points out the faint beeping sound coming from the professor's Walkman headphones. It's a distress call being sent by Skaldak. They argue about who should talk to Skaldak and eventually decide it should be Clara, since she's the only one who doesn't stink of war.
Clara approaches Skaldak under the Doctor's guidance via headphones. She salutes Skaldak and addresses him by his full title. "Grand Marshal," she begins, "I'm -- we're sorry about this. It isn't what you deserve." Lights start going out all over the sub. Clara tremblingly carries on and offers to help him. He points out he's chained up. The Doctor, via Clara, explains that it's just until they can all trust each other. Skaldak reminisces about the time he took his daughter into her first battle. It was like one of those father-daughter purity balls, but a lot less creepy. Sadly, his daughter has been dead for thousands of years. The Doctor assures him that Martians are still alive all over the universe, but Skaldak doesn't believe him. Clara, who's been slowly approaching Skaldak this whole time, realizes something is wrong, She touches his head, which flips open like a PEZ dispenser. His chest armor opens, revealing an empty cavity. "It's time I learned the measure of my enemies," Skaldak says, "and what this vessel is capable of."