Following the events of 2x12, Bellamy works with Maya, Jasper, and Monty to hide the (dwindling) forty-three survivors within Mount Weather. Maya helps them find sympathizers within the Mountain Men's ranks. During his time in the mountain, Bellamy becomes sympathetic to their plight: where he earlier was ready to suggest all-out war, he begins leaning toward a peaceable solution, in light of the moderates and children he meets inside.

He gets back in contact with Raven after Vincent moves Maya, Jasper, and Monty to a safer location. Raven and Wick help guide him to the acid fog machine (the veil, as the Mountain Men call it). Though he turns it off, guards show up, alerted to his presence in the mountain. They chase him out of the engineering bay and into the ventilation shafts where he escapes.

Bellamy continues to do work as the inside man in the Mountain, breaking back into the lab where the Grounders are held in cages. He releases one Grounder, prompting her to free the others and wait for his cue while he goes to do his part in letting Clarke and the other Sky People in. They blow the turbines, letting radiation into the mountain, which pushes the Mountain Men and their captives to the sealed level 5.

While he does his bit, though, Lexa betrays Clarke and cuts a deal with the Mountain Men. The Grounders leave, taking the small Ark army with them and leaving Clarke and Octavia alone to fight the Mountain Men.

Bellamy helps them slip inside, and they split up. Bellamy and Clarke take President Wallace captive. They get in contact with Cage and threaten him. Clarke kills President Wallace to prove they're serious, and she then tells Monty to get ready to open up the seals on level 5. When Cage sends a soldier to blast through the doors and kill them, Clarke feels their hand is forced. Bellamy supports her, throwing the lever with her that let radiation into the mountain and killed very nearly every single Mountain Man inside, as they weren't able to survive the levels of radiation present on Earth still.

They wade through the bodies to rescue Octavia, Abby, and others, and they return to Camp Jaha "victorious," but unable to stomach their own actions. Clarke, as a result, refuses to go inside Camp Jaha, exiling herself to take on the burden of their crimes despite Bellamy's forgiveness.

One of the chief evolutions these events cause in all of the characters is the realization that there are no "good guys" in war. Bellamy accepts and embraces the terrible things he's done and continues to do with the tagline of the season: "we are not who we have to become to survive." He knows that the choices they're making are in the context of a war, an us vs. them battle that doesn't have any good outcomes.

However, it also throws into sharp relief how Bellamy has changed since growing closer to and commanding with Clarke. When Lexa turned on the Sky People, she claimed she was doing what Clarke would have done, demonstrating how many characters in the show seem to learn to lead from her. Bellamy's growth is much closer to retaining the spirit of Clarke's decision-making. He sees humanity in the Mountain Men, and tries every possible peaceable outcome before resorting to the genocide. He never stops searching for an alternative solution, settling for violence and death only once their options have been exhausted and time has run out.

The man who once bullied and abused teenagers on the ground in an attempt to make himself their king through violence and force has now become a peacemaker who prioritizes others due to his empathy for them. Like Clarke, though, he was still ready to make the hard choice for their people.

Where Clarke exiled herself to deal with her grief, guilt, and shame, Bellamy did not have such a choice. When Clarke left, Bellamy knew he had to stay and help lead the people she was leaving behind. He doesn't begrudge her the choice, and he wholly understands why she needed to do it. He harbors a great deal of guilt about their actions in the mountain as well, but he's used to staring in the face of the people he's wounded. His experience with carrying that grief helps him stay among his people, as does his responsibility to Clarke (look them in the eye so that she doesn't have to, while she carries the responsibility of the choice so the others don't have to think about what was done so they might survive) and his survivalist mindset.

They've all done terrible things to survive. Whether he's looking at the Sky People or not, Bellamy isn't going to forget what he's done to get them back to Camp Jaha.