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The boys, meanwhile, deal with their father figure possibly being still with them. Dean still clings to the flask that connects him to Bobby, by holding it up and proclaiming, "Here's to ghosts that aren't there." They know they gave Bobby a proper hunter's funeral, and so it is merely wishful thinking---or so they try to desperately convince themselves. Sam coaxes gently, "Why don't you just pack it away for awhile. All it does is remind us of him, you know?" Dean nods, responding that he had thought of that, but finishes, "Just a little while longer."
It is obvious that they are still grieving, and the fact that Bobby can't seem to reach them frustrates him almost as much as it breaks his heart to see them hurt so. We can see how it pains him to see their anguish over him in the sad expression on his face in the back seat. Bobby is desperate to reach them, and demands that they look at the right time. After all he had just made that "curtain shimmy."
The bonds these three share are strong and have only been muted by the barrier of death. Even so, they are unbroken on both sides. It is no more apparent than how the brothers react to Bobby's message in the mirror. Slipping into old habits, they follow the lead that their beloved father figure has provided, making their way to solve the case.
The case itself had its own twists. The groundskeeper convicted for murdering the owner's fiancee had been framed. This is a meta reference to the storyline found in "Yellow Fever." There, too, the vengeful spirit the boys hunt has also been framed in life for a murder he did not commit. The vengeful spirit in the house that controlls everything had once been that owner---and he had been the one to kill his own fiancee. Van Ness has an interesting ability not seen in other ghosts thus far on Supernatural---he seems to be able to absorb other spirits into himself and grow more powerful.
Not unlike the fire that consumes a spirit upon a salt and burn, as he would shove his hand into their chests and squeeze their hearts, they would light up and the energy that flowed off of them would be absorbed into him. Upon discovering that Annie and Bobby had found his stash of bodies and had begun the process of burning them, Van Ness shoves his hand into Bobby's chest, trying to do the same to him.
Bobby is succumbing quickly, but the boys have discovered Van Ness's body and quickly set to work---all without knowing that they are saving Bobby's spirit from destruction. As they start to search the house afterward, they stumble across a familiar face. Somehow, in saving Bobby from being destroyed they have made him visible. They are stunned to see their old father figure---and he is just as stunned that they can see him. He whispers in disbelief, "You can see me?"
After they help Bobby and Annie put the other spirits to rest---including Annie herself---they prepare to leave the house behind. Dean and Bobby get into a conversation about the situation, and he expresses his concerns for Bobby's future. He wants to know why Bobby stayed instead of going to Heaven and drinking at the Roadhouse. Bobby remains adamant that there is too much to be done yet and that he had chosen to stay, despite the "hunter's funeral" Sam and Dean had provided. Bobby retorts, "We have work to do," a blatant shout out to the pilot when Sam says the exact same thing after Jessica is killed.
Ever the optimist and hopeful about shades of grey, Sam muses, "I mean, do you think it's possible, I don't know, we could make it all work somehow?"
It's very possible that it could. Bobby has the resources and information to manage it. He has been hunting for an extremely long time and has acquired a vast amount of information that he could tap into now as a spirit. It's good that he is now able to fully communicate with his boys---as they will need his guidance.