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(If you missed part one of the analysis, check it out here.)
In "You Can't Handle the Truth," Dean is in full panic mode concerning Sam. He discusses the situation with Bobby, considering either walking away from Sam or shooting him. He is uncomfortable, anxious, and agitated. Sam is not and has not behaved like his brother since he came back into Dean's life. He watched Sam stand idly by as Castiel tortured the young boy, Aaron, to discover that Balthazar had purchased his soul. Sam hadn't simply not raised a fuss, he had stared in open fascination. It was one major red flag for Dean that something was more than wrong with Sam.
Bobby gets Dean to hold off handling the situation permanently by saying "He's your case."
This gave Dean a purpose. If there was a chance to save Sam, Dean would take it.
Once Dean discovers what is wrong with Soulless Sam, he switches effortlessly into saving him. He might not like Soulless Sam, and this version of his brother might be all monster in his eyes, but Dean knows that it is not Sam's fault. Once he takes his aggression out on Soulless Sam at the end of "You Can't Handle the Truth," Dean patiently puts up with what ever Soulless Sam dishes.
He might be upset or exasperated by Soulless Sam's lack of care or concern in "Clap Your Hands If You Believe," but he doesn't throw in the towel. Dean has three options on the table that he could have taken at any time prior to his deal with Death in "Appointment at Samara." He could have killed Soulless Sam, he could have left him and returned to Lisa and Ben or gone hunting solo, or he could have done whatever it took to save Sam. In this case, that was returning Sam's soul from the cage.
With Dean being who he is, there really was one option all along. At this stage, it is too far ingrained in Dean not to do everything in his power to save his little brother---rather that little brother wants it or not.
What about the year Soulless Sam was away from Dean? We only learn about it through dialogue and flashbacks. It's fairly early in the season when we realize that Samuel might not quite know what to do with Soulless Sam. He is resurrected nearly forty years after his death at Azazel's hands, and thus is a fish out of water. He's trying to run the Campbell hunting family with new technology, new family members, new everything. Between 1973 and 2011 everything has changed essentially. Samuel Campbell has been taken out of the natural flow of time and inserted more or less where he does not belong.
If that wasn't difficult enough, Samuel has to contend with one of his grandsons---and not the one he met. Not only did Samuel not know this grandson before his resurrection, he is dealing with a version that is unpredictable. He does not have the insider information on what Sam Winchester was like before reemerging from Hell. All he knows is this cold, ruthless, hard man that makes him feel uneasy more than once.
As early as "Two and a Half Man," as Samuel gets frustrated about the murdering of parents and abductions of the infants, he expresses just how off he finds Soulless Sam. He senses that Soulless Sam seems not to care about the case on an emotional level. He says, his tone extremely frustrated, "You've got me wondering sometimes, Sam."
It's also the first time we see Soulless Sam question what might be wrong, too.
Samuel has a lot on his plate. He's keeping a lot of secrets. He's struggling to exist in a world without his beloved daughter. He's trying to find the Alpha monsters for Crowley, a task that must make him feel sick, but he's a desperate man. As confident as Samuel seems to those in his family, he's very insecure and quite a bit lost.
While Mary's son is in his midst, it just doesn't seem to be enough. Samuel's worked hard to put his new family around him. He has built up his compound, filling it with as many Campbells as he can get to join him. Even though he's working for a demon, it helps ground him and give him purpose. However, Soulless Sam happens to be amongst them, and it isn't hard to think Samuel suspects that he's let a monster into his home.
It isn't until "Live Free Twi Hard" that we really get to see how disturbed Samuel is by Soulless Sam's actions. He confronts him about what led to Dean being turned. Samuel knows that Soulless Sam was in on the conversation about the cure. To have him lie about it confirms the truth: Soulless Sam allowed his own brother to be turned, all without telling him there might be a cure. While he's here to deal with one grandson turned monster, he's standing in the same room with one that is much more frightening. Soulless Sam can't simply be cured by any simple long lost Campbell recipe.
Even so, Samuel tries to be the guiding force for his family. He has taken Soulless Sam under his wing in many ways, and it would seem despite his cold exterior that he's managed to somewhat gain Soulless Sam's trust. When he has an issue with a case, he calls his grandfather for advice. When he's stuck with the baby in "Two and a Half Men," despite Dean's objections, his first thought is to take it to Samuel.
Soulless Sam simply states, "Samuel. He'll know what to do."
Soulless Sam has no connections to family or others. He is incapable of forging any such bonds. Yet, he seems to gravitate towards the Campbells mysteriously. When Samuel tells Soulless Sam to hunt something, he does it. When Samuel mentions there is a big hunt coming up, it's Soulless Sam that raises his hand first. He seems to listen to his grandfather for inexplicable reasons.
It is a dichotomy that is later repeated once Soulless Sam and Dean are reunited as partners.
We don't realize just how much Samuel struggled with Soulless Sam until we see the flashback episode "Unforgiven." Samuel is struck dumb by Soulless Sam's brutality. He freezes at a moment when he should have taken action. It's probably not the first time he's felt fear being in his grandson's presence, but it might have been the first time he saw just how ruthless he could be.
As they are leaving town after a case, a local cop stops them. He is angry and confronts them about their status as federal agents. He demands that they get back into town with him and answer some questions. At first, Samuel and Soulless Sam try to talk their way out of it, but quickly the tables turn. Soulless Sam's patience runs out and he sets out to murder the cop with his bare hands. It's the most vicious thing we see Soulless Sam do, and it's probably the spark for Samuel to find a way to incorporate Dean into his hunting family.
Clearly Samuel needs help to leash this "human" monster.
We know he knew about Dean because he had met him before his death. Samuel is also smart. He might not know the real Sam by any means, but he does know how to get answers from the hunter grapevine. It wouldn't be hard for him to figure out that Dean is the key to fixing his troubles with Soulless Sam. If he can somehow bring Dean into the fold, he can turn Soulless Sam into his care rather than struggling to do it himself.
The djinn attack on Dean had to seem like a gift for Samuel. Up until now, he's had strict orders to keep Dean retired. When he saw an opportunity to reel Dean in, he took it. Samuel just didn't count on Dean's instincts or mistrust. Regardless, Samuel got what he wanted out of the deal.
Once Dean rejoins Soulless Sam in "The Third Man," Samuel is no longer the one keeping an eye on him. He no longer has to look over his shoulder with his grandson in the room. Soulless Sam has more or less left his family to rejoin his brother. Dean has effectively removed the problem for him. He only has to deal with Soulless Sam as an outsider.
Seeing what Soulless Sam does to Dean has to be confirmation of all the fears Samuel had about him. Soulless Sam wasn't just a driven hunter. He wasn't simply hardened by growing up in the life. He was a monster and part of Samuel had to feel like he had dodged a bullet in the year Soulless Sam resided and hunted with the Cambells.
There is no question that Soulless Sam had a twisted view of what it meant to be a hunter. This is partially from his lack of empathy and possibly from the mentoring he had when with the Campbells. Soulless Sam says to Dean in "The Third Man, "Yeah. I mean... I've been hunting non-stop for the past year, kind of... kind of in the wild, you know? So, yeah, I suppose I'm a little rough around the edges."
It's so much more than that.
Hunting is a rough job with no pay and little thanks. It's not a stretch to imagine that it hardens anyone who pursues it. Each hunter that the show has introduced has had some hard edge. John Winchester was a driven and obsessed man. He was the epitome of the hardened soldier. Gordon Walker allowed his hatred of vampires to transfer to Sam, turning him into a ruthless man. Others, like Rufus, become tired and weary before their time.
Sam and Dean are no different. Each one must fight their own demons---literally and figuratively. They have both experienced so much and seen so much. Sam has spent much of his life trying to leave the hunter's life behind---only to discover that there is no escape. Dean, as early as season two, exhibits his own fatigue. Both hide behind their respective masks, their edges rougher than any civilian they will help.
Even so, they both excel at it. They have their share of a failures, yes, but the wins far out weigh their losses. What makes them so successful is their compassion and drive to save as many as they can. Sometimes it leads them to make impulsive decisions that do not pan out. A last ditch effort leaves the person they intended to save dead. It's hard to say if they hadn't tried the outcome wold have been different, but that's not what matters. It matters that Sam and Dean at least tried.
In "Exile on Mainstreet," Dean rushes in to his neighbor Sid's home in an attempt to save him. He has no thought for his own safety---only the guilt that this is happening because he lived in the house next door. Dean Winchester does not know the word quit when another's life is at stake. Unfortunately, Dean is too late. He finds himself caught up in the djinn's attack a second time, until Samuel and the rest of the Campbells rush to help both Soulless Sam and Dean.
After the encounter, Soulless Sam admits that he wants Dean with him because of what he just did. It was reckless and unsuccessful, but that's not why. Soulless Sam says, "You just went. You didn't hesitate. Because you care, and that's who you are. Me? I wouldn't even think to try. "
Soulless Sam, unlike Sam, does not have the drive to do whatever it takes to save others, even at great risk to himself. He has one drive and one drive only: survive. He claims in "You Can't Handle the Truth," "Ever since I came back, I am a better hunter than I've ever been! Nothing scares me anymore because I can't feel it."
In some ways he's right, but mostly he's wrong. Soulless Sam might be able to hunt longer, more frequently, moving from one case to the next. Not having the need to sleep gives him this advantage. He's also capable of going into a situation with a level head and with a clear strategy. There is no fear in him, so he never has to worry about being frightened about his life or his family. Soulless Sam also never has to worry about anyone truly having leverage over him.
But it's those things that are a determent to Soulless Sam as well. He misses the whole point of hunting. Dean say in the first season episode, "Wendigo," "Saving people, hunting things, family business." It's more or less the Winchester motto---and it is meaningless to Soulless Sam. He misses this crucial point. Soulless Sam doesn't hunt to save anyone. He doesn't hunt out of some need to redeem himself, nor because it will help others. Soulless Sam hunts for two reasons: because it is all he knows and because he enjoys it.
We see how twisted his view on hunting really was in the episode "The Man Who Knew Too Much." Sam's protective Wall after Death had returned his soul has been destroyed by Castiel. He is trapped inside his own mind, where he meets a nice woman in a bar. Her name is Robin, and it isn't until he learns who she really is that he understands just how his Soulless self operated. In a flash of memory, Sam sees Soulless Sam face off with a demon that is holding Robin hostage as leverage. The real Sam would have done whatever it took to get her out alive, even if it meant being taken or killed instead. Soulless Sam commits his ugliest act here.
He shoots her point blank, and coldly says, "There goes your leverage."
This is not "saving people, hunting things, family business." This is murder.
Soulless Sam's other major mistake occurs in "Unforgiven." Here, they are hunting a monster not seen in America ever before. They do not know the lore as well as they might another creature, so Soulless Sam and his partner at the time, Samuel, have little choice but to fly by the seat of their pants. It is Soulless Sam who convinces the sheriff of the town to be the bait for this creature. He then lies to his face. He promises the sheriff that nothing bad will happen and that they'll be right there if something should. Before they can do anything, the monster has grabbed the bait and Soulless Sam shrugs it off. After all, they'll simply follow the GPS back to its lair.
Upon arriving, they find the sheriff and the other missing victims entombed in spider silk. Both Samuel and Soulless Sam make the mistake of thinking that these individuals will be food. The sheriff is still alive and Samuel suggests that they try to save him. Soulless Sam nixes the idea, deadpanning, "They're just dead men walking. "
His solution is cold. He simply goes to each one and puts a bullet between their eyes.
The real Sam would have been trying to save the sheriff---even if Soulless Sam's pronouncement that they couldn't be saved either from death or being turned is correct. His compassion would not have allowed it. It's the same compassion that lead to his last ditch efforts to save Madison back in season two.
Soulless Sam simply does not have this drive. It's why he's not the better hunter. All the rationality and skill does not make for a great hunter. It is a balance between the know how and the heart to pursue it that makes a hunter great.