Getting used to vault life helped make those first years distracting enough to keep things according to plan. Unfortunately, part of acclimating involved coping with some major surprises. Only a year after their arrival, Overseer Alphonse Almodovar's wife fell ill with an unknown disease. Despite frantic testing to determine the exact nature of the ailment and his best efforts to halt the progress of the disease, his patient had succumbed quickly. Expecting rage from the Overseer, he was bewildered to note the man remained a consummate politician in the wake of his spouse's death. Immediately after she was pronounced dead, he merely thanked the physician for his efforts. The only difference James could detect was in his eyes. The wary suspicion had vanished, replaced by something cold and steely.
Further research into the nature of Ms. Almodovar's symptoms revealed that in years past, other vault members had experienced similar symptoms. Whatever had caused these cases had a high fatality rate but was slow to show itself. Based on the facts he uncovered through the vault's medical computer system, the vault lost one of its own to the disease once every thirty years or so. The problem far predated his arrival at the vault and yet, in the months that followed Ms. Almodovar's death, he had a growing suspicion that Alphonse blamed his arrival for the abrupt termination of his wife's life. He began to develop and test hypotheses as to where and how the microorganism operated. Where was it going dormant? What was awakening it? As the months passed, he felt a growing sense of urgency and fear regarding the puzzle. He couldn't risk the life of his son and the lives of those who trusted him with their well being; he had to come up with an answer. So, he'd enlisted the help of Beatrice Armstrong to watch over Junior as he spent many long, grueling hours in the medical lab.
Finally, a year and a half after his arrival at the vault, he'd hit upon a solid lead. Upon cross checking the maintenance records with the medical records, he noticed that every recurrence of the illness was prefaced by a major breakdown of the vault's air scrubbing or water purification systems. He'd raced to the maintenance department and spoken with Stanley Armstrong about his discovery. Stanley had eagerly provided all that he knew about the workings of the various life support systems of the vault, and the history of repairs to those systems. Prior to her illness, the purifier connected to Ms. Almodovar's private bathroom had been fixed with parts from the repair stockpile. The two of them spent long hours gathering samples of the vault's air and water, and even began sampling the piles of materials the maintenance crew used to patch up system breakdowns. What they discovered was frightening - the majority of the repair stockpile was contaminated. Even more frightening was the fact that Overseer Almodovar had permanently severed interactions with the outside world only weeks after his wife's untimely demise. In preparation, he'd authorized the purchase of tons of repair materials, enough to theoretically last for centuries. Unless he could get the Overseer to see reason and open the vault back up to outside trading, the lives of the vault dwellers were in jeopardy.
Armed with months of research, he'd charged to the Overseer's office and insisted upon a meeting with the man. Hours later, he'd left the office unsure of what, if anything had been accomplished. Alphonse had silently listened to his arguments and stoically rifled through the papers and charts James had placed in front of him. And the only response James had been able to elicit was "Let me think about it". The long trek back to the clinic had been a frustrating one. How had the man not been immediately anxious to take drastic action? His primary purpose was to ensure the safety of the residents of the vault! When Stanley called him later to check on the situation, he sounded confused but not surprised at the Overseer's reactions.
No one but James was shocked when Jonas entered his clinic a couple weeks later and informed him that the Overseer had appointed him as James' assistant. He remembered staring at the man with a look of befuddled bewilderment as his new assistant explained the assignment. The Overseer had hoped that Jonas would be a voice of reason that would curb the doctor's "flights of fancy". He'd undoubtedly looked a mess as Jonas appraised him; arms grasping patient files, dark circles accentuating his haunted eyes, stress etched in wrinkles around his eyes and mouth. Jonas nodded once he'd finished his thoughts about his new boss, and silently stepped forward to alleviate James of his burden. His actions had a kind undertone to them, not one of pity. And over the weeks that followed, Jonas became an invaluable help; he was always benevolent and possessed a mind that was equal to James'. This made further experiments regarding the health of the vault a breeze. As the months turned into years, the two of them became close friends. When he reflected back on the early days of their collaboration, he felt guilt that he'd ever suspected Jonas of being a spy, or the Overseer's lap dog. Reading through Jonas' personnel file had shown Jonas to be the obvious choice for the position of doctor's assistant. In addition to his intelligence and superb social skills, he had no demands on his time outside of work since he was single and child free.
So their collaboration continued in the usual vein and over the years things settled into a seemingly normal routine. For James, it would never be truly normal; the threat of the repair stockpile weighed constantly on his mind. And it was that threat that eventually led him back to his Purity obsession. Fixing the vault issue was a necessity; fixing the Wasteland was his destiny. Late at night, he would pull out the Purity notes from the box hidden under his bed and refresh his memory on the project's issues and intricacies. Eventually he began sneaking into the clinic's lab when he was sure Jonas was asleep to begin actual research again. He wasn't exactly sure why he felt the need to keep his work on Purity under wraps; Jonas held no love for the Overseer and he was fairly certain his friend wouldn't think him odd. An answer came to him one day when he started thinking about the purpose of his work and the future. He'd been working on a chemical formula for dissolving irradiated particles suspended in water when the realization hit him. The Overseer irrationally refused to budge on his policy of dealing with the outside world; to him, the Wastelands essentially did not exist. This meant no messages to Dr Li and the remnants of their research team. And that just would not do.
If Jonas thought it odd that James suddenly had an intense obsession with the vault's historical records, or that his caffeine consumption suddenly reached unhealthy levels, he didn't show it. He hadn't been sure what he'd been looking for initially. From what he could tell, there were two options available to get his information to Dr. Li, and both were abhorrent. The lesser of two evils was figuring out which terminals in the vault had been granted access to the outside, and find a way to hack those terminals. He recalled one of Colin's favorite quotes then: "It's better to ask forgiveness than permission". He'd always grimaced when Colin had said it; it was so ethically questionable and he'd disliked being reminded of that side of Colin. Now he felt a vague sense of understanding, chased by a soft ache. Understanding Colin would do no good, since they'd not see each other again.
The second option was one he knew he would be unable to do, even as a last resort. Were he to come upon any incriminating information tucked away in any of the records, he could use it as leverage to force the Overseer to open communication with Rivet City. He'd been pondering how awful it was that such a course of action even entered his head on the day Jonas discovered his plans. With the last bit of energy he had that day, he finally found the entries relating to the scouting party the Overseer had sent out years ago. Anne Palmer had led the expedition to explore the Wasteland in 2241, and hadn't gone any farther than Megaton. When Jonas entered the room he didn't even hear the door open; his poor overstressed, overtired brain had finally gone on strike. He stared unseeing at the computer terminal he was hunched over, not even moving when Jonas had waved a hand in front of his face. Jonas had maneuvered him back to his room and ordered him not to come back to the lab unless he had a full night's sleep. He'd succumbed to slumber before his head reached the pillow.
And the next day, Jonas took him aside and laid his plans out as clearly as if he'd pulled them out from James' mind. He should have known better than to keep anything from his assistant; his sharp, inquisitive mind tore through mysteries as if they were tissue paper. By that time, Jonas knew him better than he knew himself; when he read the entries James had been obsessing over, he knew there was something fueling such intense interest. Jonas had told him that the Overseer had ordered several holotapes regarding Rivet City's researchers a couple months before announcing to the Vault that they would be getting a new doctor. The day Jonas had been reassigned to be the doctor's assistant, he'd gone to the library and read everything he could find on the man he would be working for. Project Purity had naturally been mentioned in several of the entries. Everything clicked into place once all the pieces of the puzzle had been identified. At the end of his discourse, Jonas had casually mentioned that he wanted in on James' plans. The research, opening communications to the outside, everything.
In his preoccupation with Purity, he'd forgotten to inform Jonas of the vault's health issues and their cause. Jonas immediately went to work on that while James continued combing the vault's history for anything useful. Then it occurred to him that Almodovar had been the Overseer of the vault for most of his life, and there might be useful information in the man's private files. It had been easy enough to remotely access his console, hack the password and gain entry to the files he sought. Most of it had been garbage - propaganda, spy reports and insipid rambling. But he finally hit the jackpot when he came across a name he recognized, Doctor Stanislaus Braun. Every scientist in the Wasteland knew of Doctor Braun, he was quite possibly the most brilliant man alive. He'd been one of Vault-Tec's researchers, and was the reason every vault was built with the most advanced technology in the world. The entry that offered up Braun's name also mentioned his work on the GECK - Garden of Eden Creation Kit. It was a terraforming module that supposedly could create life from lifelessness. These GECKs had been sent to select vaults, but 101 had not been one of them. That discovery was what he'd been waiting for; Madison would be compelled to restart Purity once she learned of the GECK!
But after he calmed down and conferred with Jonas, they decided to wait a bit longer to send their information. They didn't know where Braun or a usable GECK were, and the technical research on Purity was still sketchy. So they divided their time between Purity and fixing the vault's dilemma. Coincidentally, the solution to the vault's problem arose during Purity's research. Combining elements of how the GECK worked with James' earlier research on particle scrubbing led them to develop plans for a workable contraption that would scrub any impurities from the vault's resources. But they needed parts that the lab didn't have; Stanley provided what he could, and they got the rest by "borrowing" parts from the Overseer's private storage rooms. James' lock picking skills most likely rivaled Colin's after all the practice he'd gotten. He'd felt guilty one day when it took less than ten seconds for him to pick a very complicated lock; Colin had tried to teach him how to pick locks but he'd always turned him down. When he was young, his ethics hadn't allowed him to do such things. He'd briefly entertained the thought of what Colin would think of him after almost twenty years of ethics erosion, then shook his head to clear such thoughts. They were of no use to him.
And one glorious day, James and Jonas stood victorious over the vault's dark secret. They had caught and corrected the problem before any major malfunctions happened. With the repair stockpile cleaned, they turned their attention fully to Purity. With two brilliant minds dedicated to it, everything had fallen almost neatly into place. Nineteen years after moving to the vault, James and Jonas finally decided they had enough information that would motivate the researchers on the surface to continue and allow them to easily complete any pieces they had missed.
Almost two decades of research proved to be too much information to transmit via electronic means, however. He recalled the two of them staring dishearteningly at the hidden folder on the computer early one morning. They had used almost all of the vault's quiet time and hardly any of the information had been pushed through the line they had hacked to the outside. Jonas had been the one to reluctantly suggest leaving the vault. He'd also pointed out the fact that James would have to be the one who went to Rivet City with the files. While Jonas was very knowledgeable about Purity, he still didn't know as much as Purity's head researcher. James had refused to even listen to Jonas' idea at first - he couldn't leave his child! They were finally able to seriously discuss the idea when his assistant promised to stay behind and take care of Junior. It had taken James weeks to come to terms with the idea; while he thought, he spent excessive amounts of time with Junior, much to the teen's dismay. While he and Junior were close, his son was of the age where he'd rather spend time with friends than with his old man.
In his final days in the vault, they had obtained information vital to their plan; there was a secret tunnel leading from the overseer's office directly to the vault's exit. The tunnel would allow them to bypass the ever present guards at the door to the exit room. Jonas had gathered traveling supplies while James made sure all the Purity files were in one place and ready for transport. Once he'd made peace with the idea of leaving his child for sake of the Wasteland, he was able to figure out a way to say goodbye to Junior without making it seem like he was doing so. Though Junior had squirmed in discomfort, he'd tucked his son in bed the night before his departure. He'd gazed lovingly at the person who meant the world to him and softly asked if Junior knew how much he loved him. Junior had looked a little confused at first, then reached up and hugged his father tightly. As he'd watched Junior slip into slumber, he thought of how proud Catherine would have been of the man he'd become.
Those final hours had been hell; Jonas had ordered him to get some rest but sleep had refused to come. He'd finally gotten up and gone to the lab ahead of schedule and had been amused that Jonas had the same idea. His goodbye to Jonas had been almost as painful as parting with his son; they had side stepped those feelings by reassuring each other that every possible contingency had been planned for. Jonas would stay behind to tend to the vault residents, care for Junior, and calm the Overseer and his guards down. James had been practicing shooting in the generator room and reviewing any and all maps he could find on the Wasteland. He remembered his mind going blank as he shouldered his travel pack and they stealthily made their way to the Overseer's quarters. Of course their plan would work. It would have to.