It had been about a year. A year since the hunting trip. A year since the car wreck, caused by a semi crashing through half of a particular muscle car. A year since both the youngest Winchester's father's and brother's bodies were burned. The anniversary of it was only about 2 weeks away, but Sam had decided that it wasn't so bad. The first month after the crash had been the hardest, he had thought. What, with he and Bobby spending countless hours trying to repair the Impala, just so that they could have something to remember the two other Winchester's by. After that, his life almost went back to normal.
Sam had figured that with the Impala repaired, he wouldn't be able to go anywhere or hunt anything without immediately being reminded of his big brother. This was true, but for different reasons. Dean was borderline obsessed with his car, he drove it everywhere (not only because of his fear of flying) and made sure that any scratch on her was immediately repaired and covered up, only then was he happy. In fact, he was so attached to his car in his life, that he still seemed to be in his afterlife...
At first it had been simple, subtle even. So much so, that it was hard to tell that it was even happening; and it didn't start until after Sam and Bobby fixed the car. Sam would see something out of the corner of his eye, maybe some of the mirrors would be adjusted for someone just a few inches shorter than him, sometimes the cassette player would even switch on and play the song that was on the night of the crash.
'Don't go 'round tonight, it's bound to take your life.
There's a bad moon on the rise.
Whenever this would happen, Sam would leave the radio playing. He would intentionally leave that cassette in, in hopes of it playing. It meant Dean was there, bored in the passenger's seat and deciding to play some of his 'mullet-rock' because Sam wasn't going to put it on for him. The cassette player would immediately switch off after the song finished playing, however. Sam would then rewind it to the beginning of that song, and wait for it to switch itself on again. He tried to outsmart his brother by creating a cassette that was a repeat of 'Bad Moon Rising', but after a month of no activity, Sam figured it had something to do with that one specific cassette, not the song itself.
The activity was in small episodes at first. At first. Then, Sam found himself not paying close enough attention while backing out, and bumped into a lamppost. Immediately he felt a sharp whack to the back of his head. That was when he knew for sure. Dean was back. It wasn't just loose screws bending mirrors back to how they were, or a faulty cassette player due to the huge wreck. It was Dean.
After that, the activity picked up a bit, probably because Sam was paying attention to it, feeding Dean's ability to communicate with him. It didn't matter, the youngest Winchester welcomed all sorts of paranormal activity happening around the car; Headlights flashing on and off when it was pitch black and he couldn't find the Impala, the radio's volume turning up on one of Dean's favourite songs, his phone falling between the seats only to reappear in cup holders a few minutes later, even the constant pokes and pinches when Sam drove the Impala just a bit too roughly. Dean even made himself extra noisy when Sam wouldn't bring back any sort of pie for him from rest stops and gas stations - not that he could eat them, he'd just stare at them on the dashboard where Sam left them for him; until they reached the next rest stop where Sam would throw them out. He just liked being reassured Sam still remembered him, and it was almost as if he had never left, aside from the fact that he was actually allowing Sam to drive for a change.
The ghost, of course, wasn't an idiot. Dean knew how hunters reacted around otherwordly-ongoings. Whenever Bobby or Ellen was travelling with Sam, he quieted down a bit. He still might adjust the driver's seat position out of forgetfulness that he was no longer driving, but that was about it. Nothing that Sam couldn't cover up with a simple, "I might have accidentally readjusted it when I got out," or "It always does that - or it has since... you know..." Until the time came when he could reclaim shotgun, Dean would lounge in the backseat, only his silhouette visible to Sam looking through the rearview mirror.
It was fun, almost like a little secret the two of them shared. Sure, Sam felt guilty for keeping Dean's afterlife existence a secret from Bobby and the others, but what was he supposed to tell them? "Hey guys, remember my brother? Yeah, he's still alive and haunts the Impala, just thought you should know. He's been around practically since the crash, I just sort of forgot to mention it until now." If they did find out, what would they do? Exorcise him? Burn the Impala, or whatever he was still attached to? Sam couldn't bear the thought of it. The only reason why he had handled Dean's death so well to begin with was because he never actually left.
And that's why it was a special little secret. One that both Winchester's understood had to be kept. If Dean was taken away from him a second time, Sam knew he wouldn't know what to do with himself.
Dean hated the idea of being separated from Sam even more so than Sam hated the idea of Dean being dead for good. He didn't come back as a ghost just to make sure Sam didn't wreck his car! If the other hunters were intent on sending the older Winchester to his final resting place, Dean would be forced to do something drastic because he adamantly refused to leave without Sam.