For many readers, El Capitan is the true hero of this story. He's an evil dude turned good, and he's a hardened man with a soft interior. Oh yeah: and he acts as sort of a warped Christ figure:
El Capitan is sprawled out, unconscious, his arms spread wide, a gash on his head, his blood pooling like a dark halo. (65.8)
Check it out: El Capitan is lying down with his arms flung apart (sort of in a cross shape), his head is bleeding (much like Jesus' head was bleeding on the cross), and he has a halo. But the reason that Cap is a warped Christ figure is that this halo is dark… much like the recesses of El Capitan's psyche.
El Capitan constantly sacrifices himself; he's a martyr who refuses to die, and his selflessness is unlike anyone else's. Yet, he still has a dark side. He's not an angel, and he knows it—when he was a higher-up in the OSR, he killed innocent people. In fact, no matter how much he repents, he knows that he'll never be able to relinquish his evil side. He's caught between good and evil; he's truly a hellish angel.
The sad truth is, El Capitan can't shake his dark thoughts no matter how hard he tries—and this is partially because he's filled with self-loathing. After he kisses Pressia, he's immediately filled with guilt, thinking:
Of course she didn't want him to kiss her. He's a guy with his brother on his back, a freak among freaks. (68.19)
El Capitan's low self-worth is tragic. And this low self-esteem often leads him to feel anger. Even after Helmud saves his life from the robotic spider, El Capitan has wicked thoughts about his brother:
So why not let Helmud have at it? Helmed doesn't have it in him anyway. He doesn't have the muscularity, the timing. El Capitan would actually like to see Helmud fail. After he made that swan and gave it to Pressia, this'll remind Helmud of his weakness, his dependency, and that he should stay in his place. (46.93)
Wow, talk about hateful thoughts. El Capitan is filled with loathing and jealousy. He's a man who likes to kill, and he likes having dominion over others. He's not just misshapen physically, but mentally as well.
But even though El Capitan can't shake his bad side, but he's still arguably the most likable character we have, in part because he's willing to sacrifice himself for the sake of others. El Capitan knows the world needs heroes, and he's one of them. When an explosive device is stuck in his skin, ready to explode in only a few hours, he says:
"Sometimes people are willing to sacrifice their lives for the greater good […] We can't ask them to, but the truth is, some of them will say, Let's at least have a fighting chance" (14.121).
We're going to be both honest and clichéd here: El Capitan might not be the hero we deserve, but he's the hero we need… if only because his troubled nature, inner turmoil and self-loathing make him an awesome character.
And don't worry: El Capitan isn't just filled with doom n' gloom 24/7. When he's finally given something to be happy about, it really illuminates his struggle to break off from the past:
[…] it's like he's no longer that lonesome little boy, afraid to show any weakness, too afraid to cry even though he felt desperate and sad and lost, the one who's sure his father left because he couldn't stand to look at his worthless son ever again. For the first time in his life, he's not worthless at all. (58.87)
El Capitan has felt lonely and worthless all his life, but he sure ain't worthless now. Pressia, Bradwell, Lyda, and Partridge all give him hope. And what El Capitan gives back is dynamism, topped with a dark halo.