Starhog

If you chose Egg man's ending

(If you chose to go with the option for Egg man then this is the ending for you but if you're looking for the reset end you'll have to wait some time same for the third option if you're waiting for either one of those.)

Sonic's POV
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"Before we make a final decision for him would the reset be permanent? Is there a way to allow him to keep his memory afterwards like a soft reset? Is it painless to him?"

Tails hesitated looking at his device
" My calculations are that there's a really low chance he'd keep the memories, I have to create a new chip to replace the one he has in order to really get rid of the coding they planted within, I don't exactly have a way to transfer his memory to be stored either.. " Tails shrugged " I don't exactly know if it is painless but Gerald and Egg man succeeded on giving false memories or also wiping some off but he was only able to regain it because not everything was wiped there were parts missing but he found ways to obtain them as he was able to choose his own path to find out what he was missing. Since I have to make another chip he won't exactly have any knowledge on who he was or where he came from before he'd have a new life to start free from the torment he'd went through."
Tails tried to explain it to me  with a bit more detail this  still didn't seem right none of it sounded like a good thing looking at Shadow from a far I  really didn't think this was something he'd want to occur I figured he'd want to keep everything he knew up to this point the good, the bad, even the ugly stuff... taking away everything could mean losing everything that made him well him...  sure I'd want him to be happier and living a life he always wanted without anymore set backs allowed to grieve too those fifty years of isolation being in a pod after the death of his father must've really hurt him badly especially with the fact Maria passed not long before hand.. remembering everything he told me I knew this had to be the right choice Egg man helping had to be the one option in order to get to keep him as he is not how I'd want him to be.

" I think our best bet is Egg man I hate to say it really but he probably has a way to put Shadow's memory in a chip I can create that chip but he'll have to put everything in he most likely has a machine he can hook up to retrieve Shadow's memory like he did in the past I don't trust myself doing it like I said Shadow is far more complicated to work with since he isn't fully a machine even with the files on my tablet I still don't exactly have an idea on his workings."
Tails added looking back at me and Omega then to Rouge both were unsure but they ended up agreeing seemed Egg man was the final decision I'd need to lead him here somehow and I also may need to figure out a fair trade if he helped us I knew better than to trust Egg man completely then again with Omega standing by he wouldn't allow anything to harm Shadow I can't allow Egg man to try and use both of them as a puppet again this wasn't going to be easy... 

I left the area again getting reminded of  what I had done as I made my way to the computer room at least no one knew what I did the soldiers were on the higher levels of GUN about three floors above where Shadow's kept.
I decided to email Egg man through one of the computers once I found the room i could see some computers were turned on and also soldiers on the ground they were injured but not dead from what I could tell I made my way to the nearest computer that was on before going to emails and sending one through a soldier's account to Egg man marking it as Urgent when I'd send it to him something he couldn't over look before taking in a deep breath as I typed up the message I'd send him.

Dear Egg man, my team ran into some trouble when encountering GUN and Shadow.... Shadow is dying and we could use your help, Tails isn't sure if he can transfer Shadow's memory to a chip the commander placed a kill code on him which is in effect... We'll talk about a trade off later but right now his life is at stake. - your arch nemesis

I was in a hurry so I sent it without a second thought I wanted to sound desperate so he'd get the point he's helped us before a few times though but also that lead to some betrayal this time I was going to be watching for it also with Rouge around I felt like nothing could get passed her or even Omega Tails also was aware of Egg man's tricks he'd most likely question him on everything making sure Shadow won't be tampered with that was the last thing I needed. I sat there for a while waiting for a response but nothing came watching the time in the corner of the screen for a while until I started to grow bored I decided to look through some of the files on my own curious as to what the ones they had on Shadow, those were marked as private but still curiosity got me as I opened them I knew about the testing but seeing the videos and the research they did from past to present wasn't pretty the back injury was the worst though out of all of the history he had here what they did and continued to do was horrible  for a place that stood for Guardian Units of Nations this wasn't at all what I thought they'd be capable of they were trying to be a peaceful community one that fought a long side of me and my friends but this...  what they did to Shadow was far from guardian like. For a worldwide military and law enforcement organization that seeks to protect the Earth from all sorts of threats this just was so very horrific... Shadow was far from being considered a threat even when he was first brought in, he didn't look like a danger more like a scared child which made sense given the horror he witnessed on the ark with the raid. There wasn't really anything in Project Shadow's file that qualified as a danger other than what occurred with the Biolizard but Shadow seemed to be peaceful sure he had special gifts from chaos energy but there wasn't really anything in the file that made me think he were a danger then again I got to know him far better than these guys who deemed him as a threat after gaining the project's file I guessed they didn't read the full thing other than the biolizard, having black arm DNA and being a living weapon and a cure as a danger... ok being a living weapon did sound kind of scary but seeing the notes on how he was being raised showed Gerald didn't want others to see Shadow as a dangerous being. He was shown love and kindness even was considered to be family but it was all taken away...  seeing the newspaper clipping from the cover up they used to get the press's attention though was something that chilled me to the bone... they blamed him for it all saying he was the one to of went on a rampage killing the scientists but GUN were the saviors capturing the creature and bringing Gerald to Justice I felt Shadow was put into isolation so the truth would never be stated keeping Shadow away from public being tested on and tossed into a cell with Gerald until the man couldn't take anymore was it the sorrow of losing Maria or seeing Shadow hurt each day that caused Gerald to plot a revenge scheme the world was against both of them and no way out Gerald had no choice but to do something but ultimately ended him at least he didn't have to watch Shadow get hurt over and over.... This was enough to give me nightmares  I understood more now on what he had to deal with.
I closed out of the file unable to watch or read anymore on Shadow I couldn't bring myself to do so after seeing some of the horrible things they did only adding to my disappointment in them this was no place for Shadow.

Looking back at the email only to find no response I got up from the chair sighing before leaving the room guessing I'd check on my friends since it had been a few hours and I was starting to not regret the destruction I had caused now knowing everything they'd done I couldn't really find any remorse for what I did none of them were innocent each one did something to my friend/ rival normally I wouldn't say it but I really can't feel remorse to them  not after what I watched....
I was surprised to see Egg man though when I arrived to where everyone was like I suspected Rouge was hovering over the doctor as he worked Omega also was weary when he approached near Shadow but he didn't try to kill him given the situation Omega knew why he was there and that this was the only way to get Shadow back, Tails worked away from them hard to tell what he was doing from where I stood two robots were also helping out a long side of Egg man I stayed to the side as they worked watching Egg man's every move as well Rouge didn't seem to bother Egg man she mainly kept watch from the rafters or from above Shadow where she had sat before.

Time passed but eventually things died down and the chip was placed inside of Shadow the other one containing the kill code was out and set to a table but now Egg man focused on making some new inhibitor rings seeing how Shadow's were cracked beyond repair all four were heavily damaged that took way longer than expected no deal was made though between the two of us Tails and Rouge did the bargaining I still don't have any clue as to what he was given in return but as long as Shadow was himself I was cool with it.

An hour passed before the chip was passed to Egg man. Tails looked at Omega " you can release him from the pod now, get him to the closest table though, Egg man and I are gonna have to act fast before the kill code does anything else to him." Omega nodded I went to help him in case Omega needed a hand while Rouge watched Egg man everyone had a part in this it seemed mine was mainly to help where I could, once the door was open I picked Shadow up and quickly brought him to the closest table in the room. He was still hooked up to the machine keeping track of his vitals luckily there was a table in close range.
" alright it's ready." Tails said to Egg man who nodded and took a seat at a different table to transfer the memory into the chip Tails' next goal was to transfer the coding into it everything but the one Towers had created he was downloading each one to his device to put in as Egg man worked on the memory.
Rouge watched making sure nothing would be altered " I don't have all of his memories saved..." Tails cut him off
" I put some that I had saved from when I made him a disk drive, whatever he doesn't remember I'm sure he'll be able to gain it back."

I stayed by Shadow as Egg man focused on the memory before handing the chip to Tails, Tails took it and walked over with his tablet, " Omega I need you to cut here so I can get to the chip that's in him..." Tails pointed to his tablet to show Omega where to cut Tails couldn't do it he was afraid. " I'm leaving it to you to get the chip out and replaced." Egg man stepped in " I'll put the chip in, E123 Omega's hands are too big he could accidentally do harm."
The doctor then put on some surgical gloves after taking his cloth ones off as Omega made the incision no one tried to stop Egg man as he carefully removed one chip handing it to Omega before putting the other in without fail he had to be quick about it not wanting to find out how long Shadow would survive without the chip.
He had to be put back into the pod to heal, it was a long process we also didn't want anything to go wrong.
——- time skip—-Shadow's POV—
Vision blurred as I started to wake, nose twitched as I looked around, I could see that I was in a pod, I was able to open the door to let myself out easily I slipped out quietly only to be met by so many eyes.
Tails, Sonic, Rouge, Omega, and Egg man, each one looked at me the same way worried and concerned.  I stood confused before I knew it Sonic was embracing me his arms around me in a hug Rouge decided to join a long with Omega Tails just looked at Egg man unsure on if they should join on the group hug. The doctor just nodded to Tails before walking away as the fox walked over to join the hug.
It lasted a minute by the time everyone stepped back Egg man was out of sight guessing he was heading for where he parked the egg mobile.

Days passed but I am finally free from GUN still I have a lot to work on from the trauma but at least I'm free and alive,  everything was falling into place for once now I can freely wonder without worrying about anyone trying to control me no more missions to handle, Rouge and Omega are also free from GUN's clutches back to working with them to help keep the world safe from harm in our own way.

As for my home I still often stay on the ark but sometimes I'll visit Sonic and stay with him for a night still his home feels safe it's the only home away from home I found since staying on Earth. 
At least I'm safe now and able to roam freely like the blue hedgehog.