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John hated seeing Dean all drugged up. Most of the time Dean didn't even seem to be aware of where he was, which made it pointless to try to have a real conversation with him. Dean would lose focus after a few minutes. When Dean was first diagnosed with schizophrenia, John knew it wasn't curable, but he thought that they could get Dean stable on some meds, and then life would go back to their version of normal. It didn't even occur to him how wrong he could be. John couldn't seem to bring himself to move away after Dean had been locked up, even if Dean didn't know he was nearby John could take comfort in knowing he wasn't deserting his son. John would have never forgiven himself for leaving Dean behind and neither would Sam. Most of the time Sam tried to act like he didn't have a brother, but John could tell that some part of Sam still loved Dean, even after Dean had attacked him. Sam was the one that went to the library to study everything he could on schizophrenia, including what the statistics were for a patient to be able to live a normal life. Sam was the one that found the information showing that Dean probably really wasn't trying to hurt Sam when Dean attacked him, but instead he really thought he could help Sam. The statistics showed that most people with schizophrenia don't hurt other people, and Dean had always cared about Sam. John wasn't sure if that was true or not since the one time he tried to ask Dean about it, Dean had just given him a blank stare. Of course, a blank stare was Dean's response to almost everything. John found himself wondering if he was to blame for Dean's condition because living the life he had forced his kids to live couldn't have been easy on either of his sons, but especially Dean who had always taken on more responsibilities.
John was able to find a job at a local garage that paid pretty good. He wanted to try to make up for his mistakes with Dean by not demanding as much from Sam. As far as John was concerned, Sam's main focus should be on school, so he started keeping Sam out of anything to do with the supernatural. John still looked into supernatural things in his spare time, but he passed along any jobs he found to other hunters. Now he had become the person other hunters called for information; it was a complete role reversal. John still hoped to be able to go back to hunting full time at some point, but he didn't know when that would be. He was determined to put his sons first, after what had happened to Dean. The first time he told Jim and Bobby that; they both thought he must have been possessed, which didn't help him keep from blaming himself for what had happened, but if he had been completely honest with himself, he figured he probably deserved that reaction.
When John had told Sam to focus on school he hadn't even thought of the fact that it could lead to Sam moving away. He figured that Sam may have wanted to go to college, and as far as John was concerned if Sam paid for it himself, he was welcome to go. However, he had been thinking about a college nearby, not one on the other side of the country. John had hoped that Sam would stay close by to help keep an eye on Dean once he was released, and then after they were sure that Dean was okay John had been hoping that they could at least go back to hunting part-time.
When Dean turned 21 John tried to get him released, but the drugs kept Dean from realizing that he shouldn't talk to the doctors about supernatural things. Every time Dean brought it up the doctors stayed convinced that the medications weren't working and would decide to keep Dean longer. After Sam left for college, John started going to see Dean more often. Part of the reason he started going to see Dean more often was that Dean hadn't taken the news of Sam leaving very well. Dean had finally started to show some improvement, until Sam had left. After that, Dean became depressed and thought he was to blame for Sam leaving. John didn't tell Sam about it because he didn't think it would benefit anybody, and it would probably make things worse. Instead, John tried to make sure Dean knew that Sam leaving wasn't his fault, and eventually Dean seemed to believe it. John was finally able to convince Dean not to mention anything supernatural to the doctors, and on Dean's 23rd birthday, he was released. John had looked forward to that day for several years and used his vacation time to spend the next week getting Dean settled into the apartment they would share. John had arranged for Dean to work part-time at the garage with him after Dean was settled. Dean's schedule for taking his medication allowed him to be coherent during the day, while the medication he took at night left him out of it, but by morning he was back to functioning again. John had created a chart to keep track of when and which medications Dean was supposed to take and kept it posted on the refrigerator.
Dean seemed to enjoy working at the garage with John, and since Dean's release, he hadn't been showing any symptoms. Dean's psychiatrist had told John after one of Dean's appointments that she was amazed by how well he seemed to be doing settling back into life outside of an institution. Dean still didn't talk much to John about how he was doing, but Dean had been that way ever since Mary died. Dean occasionally asked about Sam, but John hadn't talked to Sam after he left. Since Sam had first researched schizophrenia, he had always been concerned that he may develop it since Dean had it. John couldn't totally blame Sam for wanting to run away and get a fresh start because of it. John wasn't going to force Sam to contact him, but he had made it clear when Sam left that he was free to contact John if he wanted. It was John's way of trying to give Sam the freedom he desperately wanted.
When Dean was 25, he caught a cold that developed into bronchitis, which meant that he was prescribed several different medications. By that point, John had become comfortable with letting Dean keep track of taking his medication and getting refills of it from the pharmacy, but apparently with the added expense of the medication for bronchitis Dean decided to stop taking his other medication. John had noticed that Dean had become even more distant, but had put it down to Dean being sick. One Saturday afternoon in October, John came in from going to the grocery store and found Dean in his room with one of John's handguns that he had kept in a lockbox in his room. John didn't know how Dean had found the key, but that was the least of his concerns at that moment. Dean currently had the gun aimed at his own head. John ran across the room and reached Dean just as he was pulling the trigger. John managed to knock Dean's arm enough to change the trajectory of the bullet, so it grazed Dean's temple before lodging in the wall behind him. John grabbed a t-shirt that was lying nearby and pressed it to Dean's temple to stop the blood flow, with his other hand he got his cellphone out of his pocket and dialed 911. While John was talking to the dispatcher, Dean kept saying it was his fault that Sam had left and that if Dean weren't around then Sam would come back, so John wouldn't have to be stuck alone with Dean. John tried to reassure Dean that Sam didn't leave because of him and that John loved Dean and wanted him there, but Dean didn't seem to be listening. It didn't take long for the paramedics to arrive and they soon had Dean ready for transport, telling John before they left which hospital they were taking Dean to, so John could follow them in the impala.
After waiting for several hours a doctor finally came out to the waiting room to talk to John, he explained that they had run tests and that there wasn't any permanent damage done by the bullet. The blood work that had been done had shown that Dean didn't have any of his prescribed medications in his system, which probably accounted for the suicide attempt. The doctor also told John that they would keep Dean overnight for observation before transferring him to a mental hospital that would help get Dean back on his medications.
Dean stayed at the mental hospital a week before he was released.
When Dean was back at home, he didn't discuss anything about what had happened, and John didn't want to force Dean to talk about it if he didn't feel like it. John was sure that Dean's doctors were already making him talk about it. He did make sure that Dean knew he never had to go without his medications for any reason and to let John deal with finding a way to pay for them. Once Dean was cleared by his doctors, he went back to working at the garage with John and soon fell back into his previous routine.
Shortly before Halloween in 2005, John received a call from a hunter, but it wasn't the kind of call he usually received from hunters these days. Instead of giving the hunter information, this hunter gave John some information that he said explained what had happened to Mary. John didn't feel like he had any choice but to go back to Lawrence to investigate it, but he didn't want to put Dean through the trauma of going back there. He told Dean he was going to help Bobby with a hunt, but he would be back in a few days. John thought if he told Dean that he was with Bobby then Dean would call Bobby first if he started having any problems and couldn't reach John. John arranged to take a week off from the garage and left on a Friday night right after work. He had made sure before he left that Dean had plenty of his medication, even though Dean accused John of treating him like a baby and not trusting him, but John didn't want to take the chance of Dean running out of it and not spending the money to get them refilled while he was gone. This was the first time John had left Dean alone for any real length of time since the time he had left Dean and Sam when they were teenagers and it had gone so horribly wrong, so John thought he had a reason to be extra nervous. John decided to drive the truck he had bought through the garage since it was more practical than the impala for one person and he didn't want to put unnecessary miles on the impala. They lived close enough to the garage that Dean was going to walk to work and take the bus to his doctor appointments while John was gone since Dean hadn't ever gotten his drivers license.
John made it to Lawrence, but he hadn't found out much and was beginning to think this trip was a waste of time. He had been calling Dean nightly to check in with him and everything seemed okay, but Thursday afternoon he received a call from Dean's doctor informing him that Dean had missed his appointment and did John know why. When John tried to call Dean, he didn't answer his phone. John hurried to pack up all of his stuff and headed for home, all the while trying not to think about all the things that could have happened to Dean that would be keeping him from answering his phone. When John made it back to their apartment near Dallas, he found most of Dean's clothes packed and the impala gone, John's extra stash of weapons was also gone. Thankfully, Dean's medications were also gone, which offered John some comfort even if it didn't guarantee that Dean was actually taking them. It had been after midnight when John made it back home, but he called both Bobby and Pastor Jim to tell them to keep an eye out for Dean and to call if they heard anything. Even though John didn't want to, he knew he needed to get a few hours of sleep before he went searching for Dean in the morning. He set his alarm clock for 6:00 and tried to go to sleep. After all the tossing and turning during the night he only managed to get about two hours sleep, but John still got up when his alarm went off. He turned the coffee maker on before getting in the shower, so he could take a cup of coffee with him when he went to look for Dean. John went to the garage first and found out that Dean hadn't shown up for work since John had left, and they had just assumed that Dean had decided to go with John at the last minute. After spending the whole day searching for Dean without any luck, John decided to head back home and start fresh the next day. John had thought about calling Sam, but it was a Friday night and he figured Sam was probably out, besides John wasn't really looking forward to telling Sam that Dean had disappeared while John had left him alone for nearly a week just so John could follow a lead.
John finally decided he needed to call Sam, so he searched online and was able to find Sam's phone number but with the time difference, he decided he had better wait until after 10AM to call Sam. He didn't think waking Sam up early on a Saturday morning was going to help his case any. John didn't want to waste time on an argument that could be avoided. When John did call the number a girl answered, and after he introduced himself she told him that she was glad he was okay because Dean had shown up last night saying he was missing. Sam had left with Dean to look for John, but they would be back before Monday. John was even more confused when he got off the phone than he had been before, but he knew he needed to get to Stanford, so he could be there when his sons got back.