Doctor Who has had a long streak of pacifism. Arguably, this streak became the strongest during the Pertwee years. This may be the biggest difference between the first two Doctors and the Third Doctor: violence. The First Doctor, let’s not forget, was eager to brain an injured Neanderthal just to convince Ian, Barbara, and Susan to return to the TARDIS. The Second Doctor would put companions and innocents in danger just to gather more information. While it is still too soon, at this point, to determine this Doctor’s views on violence, he seems to have turned a more critical eye toward it.
And rightly so. The Doctor is stuck on Earth. He is the lone Time Lord on a planet full of primitive (from his perspective) people. Sure, he likes humans, but they are not his equals. Thus, when a UNIT soldier opens fire on a humanoid creature in the caves surrounding the research center, it is a bad sign. First, there is no evidence the creature meant any harm. As The Doctor points out, it may have been calling the dinosaur creature away from the soldier. Second, it is a signal that the alien, in any form, is other. Perhaps it is best to shoot first and figure out the truth later. This implication puts The Doctor in danger. His human appearance, in this case, is his best defense. The Doctor has every right to cast a critical eye on the military tendency to attack because, if circumstances were different, he would be the enemy rather than the ally.
The strength of The Brigadier’s character is that he must mediate both worlds. He is human and he is defending England (at the very least) from alien attack. His first two experiences with aliens were negative. UNIT was born in violence, not peace. While The Silurians—and later threats—may not be on par with The Great Intelligence, they must still be approached with caution. UNIT isn’t Torchwood; they do not have technology to compete with civilizations that can traverse space and time. And just how does the military repel an attack from the astral plane?
But The Brigadier has a great ally in The Doctor. He must protect that working relationship, that friendship. The Doctor must act as a conscience to temper the military side. The Brigadier, unlike some military minds in Doctor Who, allows this conversation. He is willing to listen, to take advice. This is a new dynamic for the show.