The Reader is Jonathan's assistant and both of them share a good friendship, However both of them also secretly have strong feelings for each other and had hope that she would change him from his fearing ways

Sorry that it is really long I kind of got carried away a bit by either over explaining or too many ideas and how to phrase it so sorry if I went off the rails for the plot or twisted it slightly, but I still hope you like it

For QueenZain3  

Fandom: Batman Begins {Christopher Nolan collection}

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Throughout school she had always wanted to be a psychologist like your friend Harley but she decided to live her life in a different way before getting a job which meant constant parties while you stayed in your room and studied your life away

When you eventually got a scholarship at the age of 25 since most people had to get thorough checks to be in a place like that you thought that it wouldn't take that long but soon after a while Johnathon took you on and after the first week you both shared a healthy friendship

Most people has assumed that Johnathon had started to fall for you and for some reason they either went missing or got mentally ill then got sent to Arkham but you didn't realize it since it wasn't on his list of patients which he went to see today

"we have Jim who suffers serious PTSD fearing that he is in a zombie apocalypse and people are trying to kill him with a weird virus" you spoke out reading his file and Johnathon nodded as he listened to you intently as you read off his file ignoring the people around him for attention unless it is for security

"well does the medication we give him work or do we need a stronger dose?" he asked as you both went through the protocols of security

"they are working fine but nurses are claiming that he's not actually taking them as of late" you read before setting the file down closed and went through before picking it up again and continued before switching to files of the other patients as you went to his office and talked the rest of the day but he mainly sat and admired you as you spoke

You both had worked together for a year even after your scholarship and even people on the outside knew he liked you and told you that but you didn't see it and or didn't believe them but it wasn't your main concern though it didn't stop you thinking about it

When you got home you realized you forgot some paperwork that Johnathon wanted you to work on but since you wanted to keep your job you went back to the office to get them so you could finish them behind a nice cup of coffee and the sound of rain hitting your slightly expensive apartment

When you got to Arkham it was eerily quiet than what your used to hearing but maybe that's because your used to people walking around and or Johnathon being near you but you still pushed through not wanting to seem weak in front of the men in the building and went to your office you shared with him

As you picked up the file you sighed slightly and decided to do it there since Johnathon had his papers on his desk so as you worked you heard the typical screaming from inmates but you shrugged it off since you were in the petitionary you kept hearing screams and incoherent mumblings every so often

After a few hours of working there you heard a scream from one of the new patients on his list that he had refused you to meet and he refused to give you reasons why so you looked at the files on his desk and wrote down the cell numbers of those patients and decided to check on them and on the last patient that was on the list you heard the screaming was more prominent and upon your better judgement and your curiosity got the better of you and you went to go look

But when you got to the cell you saw a man that was Johnathon's height and figure but you weren't sure if it was him or not with a scarecrow mask on but upon further inspection you clicked that it was due to the suit since you bought him a similar one for his birthday and gasped in shock as you saw him spray green gas in the patients

"Johnathon what are you doing!" you exclaimed making him shoot his head towards you in shock dropping the small bottle in his hands and turned to you taking steps towards you but you stepped back in fear something he never wanted you to be in when you were with him

"it's not what it looks like Y/N" he spoke as his face was pale in fear himself but you couldn't see it due to the mask being on his face but he scared that you wouldn't go near him again and leave the workplace to go somewhere else and he couldn't have that

"your making patients be afraid of their conditions? Why? It's not legal to do that..." you spoke out stepping back more and more away from him before bolting it down the halls and Johnathon chased after you not wanting you to tell anyone and wanted to make sure things between you two didn't falter

After 20 minutes of running since your mind wasn't letting you think of the right way to leave the building Johnathon eventually caught up with you

"I'm sorry Y/N" he whispered sadly but sounded deeper due to the voice modulator on his mask so it didn't sound as he intended it to sound before he pulled a needle from his suit pocket and sedated you slowly pulling you to the floor so you didn't hurt yourself

After a few moments he went back to the cell he was at and made sure everything was locked up before picking up his things and took you both out of the building making up an excuse to the guard that you were too tired from working which worked in his favor as the guard didn't expect anything out of the ordinary

Around 3 am the next morning you woke up in a room at first you didn't realize whose it was a first since you were dazed but as you came to your senses your realized it was Johnathon's bedroom and the memories from earlier came back to you and fear had set in again but still tried to process what the hell happened in the Asylum

Not long after Johnathon came in the room with some food and water in his hands for you since he knew you would be slightly hungry or thirsty he didn't know so he brought the latter but when he walked in your shot up from the bed and moved to the other side of the room to get away from him hurt him more than what he was already feeling beforehand

"I'm not going to hurt you Y/N that's the last thing on my mind" he spoke out sounding heartbroken as he watched you before setting the tray on his bed gingerly before backing up slightly back to the door so he doesn't scare you any further

"like you didn't hurt the other patients that we were trying to get better!" you yelled slightly but he knew that was only out of fear not out of anger "you were reversing the progress that we were fixing!"

"but I would never hurt you that is the last thing I would ever imagine of doing" he explained as he looked down hurt that you thought he would use the gas on you "I'll let you get some rest and some space I'll be back in a little bit" he said after a bit as he looked down and walked away shutting the door quietly as you relaxed a bit but not completely as you eyed the food and the glass of water not trusting it thinking that he would've done something to it but as you were thinking to yourself you heard some slight crashing and banging in another room making you jump slightly

After 30 minutes you slowly left the room and walked to the living room quietly and saw him sitting on the couch mumbling to himself upset of how he made you feel and more inspection of the room you noticed some stuff had been thrown to the floor in annoyance but the only thing that was left untouched was the picture of you two together in front of the asylum when it opened up and another when you both won your first case which confused you a bit but didn't say anything letting the theories fill your head silently since it was the least of your worries

After a few moments slowly padded across the room quietly and sat on the couch in front of him and watched him cautiously "Johnathon..." you whispered softly but his head shot up at the sound of your voice making you jump slightly at the sudden motion "why did you do it?" you asked after a few moments of watching him

He stared at you for a few moments before composing himself slightly as he sat up in his seat a bit making you now notice his red eyes that he had been crying which broke your heart since you didn't like seeing him upset at the best of times but he cleared his throat and explained why he does what he does to the patients with his homemade fear toxin

As he explained what he did you listened and you tried to keep your cool on the outside but on the inside you were terrified of him and what he did to his patients so you backed up in your seat slightly to get away from him and just from that you could see his heart break in his eyes even more

"as I told you before I would never ever use it on you you're the last person I would use it on even if you asked me to do it I would refuse" he spoke out as he tried to reach for you hand to comfort you but you moved your hand back and so did he awkwardly knowing the relationship between you both were now strained despite the love he held so dear for you

After a few moments of silence, you slowly got up and silently headed out of the house and he didn't stop you since he didn't want to make you more uncomfortable and keep you here against your will

When you got home you took a hot shower but even after you had your shower you sat in it and replayed the events in your head which made you shiver in fear but despite the fact that he has done those things you still felt the love you had since the first week you had met him

A few days after the incident you had went to work as normal but a different psychology professor which you didn't like due to the fact he acted like a creep half the time to the girls here came up to you with new files making you look confused

"I'm sorry you must have me confused with someone else I work with Dr Crane" you chuckled awkwardly as you handed them back to him before moving to go to his office but he stopped you again

"sorry Dr Crane had assigned you to me for the forceable future so you don't work with him anymore since he got a new assistant as well" he explained as he watched you but as you heard the news it broke your heart that he just replaced you like that but after a few moments anger started to bubble so you turned around and stormed into his office

"Y/N please leave you-" Johnathon started as he saw you standing at the doorway with anger but he saw the slight upset nature in your eyes which most people would've missed but you glared at him before cutting him off

"you shut the hell up and you leave" you spoke out annoyed to him at first before looking at her who stood close to him at a more couple standpoint then an assistant and pointed to the door

"I'm afraid you don't-" she started but you took a step closer to her in a threatening tone

"I said leave" you growled slightly making her jump and leave but before she even got out properly you slammed the door behind her before turning to Johnathon again

"Y/N you don't work for me anymore you can't just barge in here" he spoke out with a small sigh trying to get you understand him without him yelling at you while standing up from his desk and walked around it so he was standing in the middle of the room

"so that's it? I see your crazy little side experiments and you just toss me to the curb for someone else to deal with?" you replied annoyed as you took a step towards him "that doesn't work for me because he will treat me as some side piece and you know that" you added annoyed as he looked at you with the same look a few nights ago

"I'm doing this to protect you from what I'm doing so that you don't get involved with this" he replied as he took his glasses off to rub his eyes probably from the lack of sleep he had been getting about thinking of you and how he screwed your life up before putting them back on his face

"I don't need protecting from your stupid project because I know you won't use it on me as you have stated so who do I need protecting from? Batman?" you shot back annoyed as you stood back in your stance and crossed your arms annoyed

"most likely since he doesn't want me to continue my work finding it inhumane and lethal to them" he replied back as he looked at you "just please drop this I won't stop when I'm in a middle of a massive breakthrough I almost perfected my research and created the perfect toxin for them" he replied in an excited tone but you didn't seem happy about it as much as he was

"Jonathon you can't just keep doing this...your hurting people...and your messing with their mental stability you can just keep doing this...fear is something people have even if they don't need to realize it" you replied back pressing a soft hand to his cheek

"no, I'm not stopping my research because you don't like it this is my life's work" he replied pulling away from you with a scowl on his face making you look hurt so you backed up from him

"then I can't work with you anymore...I don't want to work with someone who hurts the livelihood of Gotham city..." you whispered as you backed up from a bit more before setting your id and everything on your 'desk' and walked out while he watched you hurt but also with a mixture of 'I think that would be best'

During the rest of the week, you had started to work for Wayne industries as his secretary and he knew that it would be short term but he knew the circumstances since he has met you more than once but despite being scared of Jonathon you couldn't do anything normal since you were used to his presence being near you and his mannerisms

So, one day you had enough and went to his house and knocked on his door but it only took a while for him to get there and opened it to see you making his smile drop a bit which confused you before noticing the mask handing out of his pants pocket

"not safe to come in?" you asked after a bit with your eyes lingering on the mask in his pocket and he shyly nodded while trying not to let most of the chemical smells get to you despite it being 4 rooms away from the front door "you can't just keep doing this Johnathon" you said softly as you looked at him who looked more disheveled then the last time you saw him as if he couldn't stand not being near you either despite it being 4 days since you last saw each other

"people need fear in their lives" he shot back calmly since he didn't like fighting with you at the best of times so he tried to avoid it the best he can especially after you just suddenly quitting your job and not coming back he wouldn't care if you stayed and it was in a different department or having patients of your own but you left completely

"yes and they already are afraid by the fear in their lives but some choose not to face it head on like others do and they don't need to be reminded of it either" you replied back and he shook his head annoyed as if you were trying to change him

"you know what I meant ok I love you too much to let you get involved or lose your perfect career choice over something I'm doing!" he shot back angrily taking a step towards you opening the door slightly not yet processing what he had said but you did "and the last thing I want is for you to lose everything you have worked hard for!" he added back raising a hand for expression but you stood there on his porch shocked

"you love me?" you replied calmly but quietly as your arms dropped to your sides as you watched him lose his anger as well and looked at you in the same way but had a slight blush on his face ignoring the conversation that we were just talking about

"y-yes..." he replied after a bit "have ever since I saw you come into my office for the first time I tried to hide it at first but seeing as people were fawning over you left and right I thought they would be better for you" he added after a bit looking down shyly

"well, they did try and ask me out but I refused them since I had someone on my mind anyway" you replied as you walked over to him which ensued you being in the house a bit and lightly rested a hand on his cheek which made him look at you softly

"you did?" he asked confused mainly at why you rejected them but also at who the other person would be since he hadn't seen you with anyone else but the people in the office and your family which was rare but it made him happy that you had shared the same feelings for him all this time

"yes because the person I thought didn't like me was all shy and weird and always had his nose stuck in a pile of papers" you replied with a small chuckle as his now red face "but I couldn't blame him though because at the time he pushed half his pile of papers in my nose too so I didn't see it much either" you added as you watched him with a shy smile which he returned after a few moments with a blush still on his face

"maybe I should've stop shoving piles of papers in your face then" he chuckled slightly as he hesitantly rested a hand on your hip as you leaned into his touch but soon back off of you after realizing you know him as the monster he has now became "but this can't work..." he replied after a bit making you frown

"why not?" you asked a little heartbroken at the sudden change in his attitude as you watched him back away more into his house to either get away from you or to make sure you didn't see him you didn't know

"I'm a monster and after finding out what I do that's going to push you further away from me than before and I can't have that not after what you saw" he whispered as he looked at you hurt

"you're not a monster you just have different views on the world than other people but you can stop doing this I can show you that there is more to life than just fear" you spoke out as you rested a hand on his cheek "just let me try" you added with a soft smile and a slight puppy dog look in your eyes

"ok but I don't think you can take a monster away from the source" he spoke out with a soft sad smile as he rested his hand on your hand that was on his cheek and leaned into your touch making you smile even more

"I beg to differ" you chuckled softly as you looked at him with challenge in your eyes and he chuckled slightly at the sight but didn't object to it but mentally thought 'challenge accepted'

A few days had gone by and Bruce decided that you should take a few days off so as you paced your apartment I thought but soon got an idea that might break or mend your already unstable friendship you had with Jonathon so you sighed grabbed your things and put them in your car before heading to the asylum to where Jonathon was sitting at his desk working since his new assistant was out probably

"Jon get up your with me today" you spoke up as you watched him give you a confused look which you found adorable since he looked like a slight puppy so you fought back a smile as you looked at him with a slight stern look

"what?" he replied confused at mainly the nickname than anything as he sat up straight as he made a 'go on' motion with his hand as he went back to his work fighting the urge to just agree with you there and then

You watched him for a bit then let out a small huff before grabbing his files and walked out the room with a small smirk knowing he was following you with the odd occasional looking behind him but that didn't stop you from getting to your car that was near the entrance of the asylum gates far from the entrance of the building

"good you're out your office now you can come with me" you replied as you set the files in the back seat in a special box that you made for him and looked at him who chuckled slightly at your attempt

"Y/N I need work to do I can't just skip a day" he replied as he tried to get the files from your car but you shut the door with your body and stayed there leaning against the car as he stood in front of you with his hands on his hips

"just one day and if you hate it I won't do it again just one day" you said softly but as you said the last 3 words you fixed up his jacket and tie slightly before looking up at him innocently

"fine one day" he spoke out as he watched you knowing he would've agreed regardless but wanted to put up a little fight just to see you act a little stubborn which he found cute about you but got in the car just to entertain the thought of you wanting him to skip work

By the end of the day, you could tell that he would do this more often as you watched him head back into his house with his files in hand with a smile on his face but as he got to his door and you drove off he just now realized you took him on a date and turned to the direction of where you left in shock for a few moments before a soft smile turned on his face knowing he would have to get you back for this

You kept up this act when you had days off or when you got off work early and at some points he was expecting it and others he was just as surprised the first time but he did get you back though on some occasions he had found the right place to go to

After the 6th date you could tell he was still working on his project due to his ruffled hair which you may have found cute but you knew that it was from stress so you worked with Bruce a bit and he purposely 'gave you more work' which meant staying back late knowing that you could've done it at a later point but he wanted to help you since most people shipped you and Jonathon together

Since you were 'staying at the office so late' you hardly had time to plan anything with Jonathon but it's not like you were thinking of it either so Jonathon kept working as normal but when he doesn't receive the surprise visits and the constant texting from you during or in the middle of the night he started to miss your presence

At first he shrugged it off thinking you were just busy but as the days went on he started to miss you a lot more than he should have which made him look at his lab every time he went into the room with disinterest but kept looking at his phone waiting for your text or call which always made him leave the room and back into the living room or his work office

After a few hours had passed he huffed and set his phone on the large pile of files on his desk and fixed his jacket before heading out to your house with his hands gripping the wheel tightly

When he arrived, he got out slamming the car door behind him and knocked on your door making you answer it calmly

"oh, hello Jonathan? What brings you here" you asked slightly shocked but instead of him answering you he pulled you closer to him with one hand while the other was on your neck and roughly kissed you making you jump a bit by resting your hands on his chest but kissed back nonetheless

After a few moments you both pulled away to breath but you looked up at him confused whiles having a faint blush tinting your cheeks at his sudden boldness but you didn't remove your hands from his chest

"you win" he whispered as he looked you like he had just obtained the only thing that could bring him unlimited happiness for all eternity

"I win what?" you spoke confused as you looked at him before slowly fixing his hair a bit and he relished in your soft touch

"you win the fact that I can't do anything without you by my side I can't live without you and if that means quitting my side hobby for you then so fucking be it" he muttered before kissing you roughly again for a few moments before pulling away

"then I guess I should go back to my normal work schedule let me just call Bruce" you teased slightly pecking his lips before walking back inside to grab your phone while he stood there shocked but chuckled as he walked into your house and shut the door behind himself and followed you around the house with a small smirk on his face

He left his other house and kept up with the monthly payments and locked it up after moving in with you and you knew he kept the other house where his lab was but you kept the key to that place with you in your desk at your office in a small biometric box that Bruce made for you

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As an apology for it being so long and delayed here is a cute picture I found