I don't own detective Conan if things seem off they probably are and I'm sorry but I'm going off of what I've read and seen

Well things were going ok at the moment Shinichi and Haibara were even closer to getting a permanent antidote to the drug they had taken that had shrunk them and they hadn't heard from the Black Organization for a while but at the same time things weren't going so well because Jodie an FBI agent that's currently in Japan was pretty much seeing her dead partner wherever she went only he now had a scar on his face and currently couldn't talk either that or he wouldn't but she wasn't sure which it was of course everyone else was telling her that he was dead

"hey Conan where do you think you're going?"

"to Agase's house Ran-neechan"

"fine but don't be too late getting back for dinner"

and so he starts heading towards the professor's house when suddenly he spots two members of the Black Organization and that was pretty much trouble and he knew it so he used every trick he could think of to escape and ended up being grabbed and pulled into an ally where he fought the person who had a good hold on him until he was knocked out. Hours later he woke up with a headache and also knowing that he was extremely late to dinner

"look whoever you are by now Ran-neechan will have called my phone and if I don't answer it she's going to get worried"

"I know that however I told her that you're going to stay at Agase's for dinner"

Shinichi is shocked that the person knew where he had originally been headed but was also wondering why the person's voice was so scratchy as if it hadn't been used in ages

"ok who are you and why have you taken me prisoner"

"who I am isn't really important right now as for taking you prisoner" (scoffs) "it's quite the opposite actually I saved you from the Black Organization when I grabbed you and knocked you out"

well with that said Shinichi tries to use his tranquilizer watch but finds that it wasn't working

"don't bother I already made sure that thing doesn't work before you woke up same goes for the rest of your tools now then you must be hungry by now so how about some dinner"

and with that the person is finally seen in the light for the first time but unfortunately it's a bit of a shock for Shinichi and thus makes him faint from shock a few minutes later he wakes up and vocalizes his thoughts

"how can you be here when you're dead?"

"I was never killed our inside person faked my death really well and since then I've been keeping an eye on you guys albeit as covertly as possible"

"and I'm safe to assume your voice is due to the burn on the side of your face right?"

"that you are"

"well then Akai Shuichi welcome back from the dead"

after that they eat in silence but once that's done they actually start doing a little bit of planning but not a whole lot and certainly not very effective planning seeing as how they were forced to come up with one within an hour

"ok I think I know how to proceed now"

"ok how?"

"first of all I'm going to tell you my real name isn't Edogawa Conan"

"than what is it?"

"Kudo Shinichi"

"the high school detective that's been missing for quite some time I'm impressed you've managed to live this long"

"so am I actually"

"so what's your plan?"

"simple we get the guy that's currently in my house out and get you in"

"think he's an Organization member?"

"not completely positive but he's been creeping Haibara and I out for a while and has been acting suspicious I say it's time he leaves my house"

"than let's do it, tomorrow"

"yeah I'm already late getting back to Ran and in any case we're both extremely tired so we really can't do anything about moving you right now but tomorrow night we will"

"what about Haibara?"

"she doesn't find out for now and neither will my parents or the FBI unless you want them to"

"good idea I know for a fact that Jodie would kill me if she found out I've been alive this whole time and haven't been in contact"

"exactly"

and so Shinichi goes back to Ran's and the next evening they get the one person in and Shuichi replaces him

"well part one of the plan is in place now for the rest of the plan to come together"

"what plan?"

"oops forgot we don't have a plan yet"

well they actually manage to come up with a decent plan between the two of them when the FBI made a move against the Organization without Shinichi realizing it and all of the officers were either dead or critically injured plus the Black Organization basically claimed leadership of Japan

"Conan-Kun where are you going?"

"I'll be back"

unfortunately he wouldn't be back and they wouldn't see each other for five long years during which time Haibara would find a permanent cure and find out that the new guy was an FBI agent. Five years after the Black Organization had taken over Japan

"ok so Tokyo has supply routes as does Osaka and a few others"

"great how's Hattori-Kun anyways?"

"fine very glad I'm able to stop adding niichan to his name and can also just call him by his last name in public like I did whenever we were alone"

"good"

"any news on Ran and her family?"

"not really though I know for a fact that she's alive and recently Jodie and a few other FBI agents have joined up with them but that information is five weeks old now"

"and of course no one but us knows that you're the 'dead' Akai Shuichi"

"naturally"

well things were not going well for Ran and the others with them they had little food practically no water and to top it all off they were currently in Black Organization infested space

"ok so now what the Black Organization has decided now to do the resistance sweep"

"I have absolutely no idea"

well Jodie was by herself when her boss came over to her

"what are you thinking about Jodie?"

"that if only Shuu were here we'd be able to make up a good plan"

"Jodie…"

"I know he's dead but boss you have to understand that up until the Black Organization took over both Camel and I thought we saw him, he was burned and didn't talk but it was him"

"we'll get them back for that Jodie I promise our inside person recently contacted me and mentioned that they can't get to their superiors at CIA since America has also been taken over recently"

"well what did they have to say?"

"easy apparently there's been a ghost stealing from them and they're starting to get a little panicky"

"a ghost?"

"yes one Kaitou Kid I believe"

"ah the infamous thief that always toyed with the police and up until people started shooting at him he had the policy of no one gets hurt"

"exactly though people have used that to their advantage a few times and killed in his name but those people are quickly taken care of"

"I take it he never liked people using his name in that way"

"you've got it he's gotten payback every time someone does it plus he has a few supporters that fight to prove his innocence"

"so when they thought they killed him five years ago in his last official heist he somehow managed to escape actual death and has started to steal from the Black Organization"

"yes though how he manages we have no idea"

Ran walks over

"hey guys I think it's safe to move again, how about we go to Shinichi's old home and stay there for the night seeing as how it's the biggest place I can think of not to mention we'll be a lot safer there than at my dads old detective agency since they really had no idea where Shinichi lived"

"then let's go"

and so with the cover of night they move to the Kudo home only to find that people already lived there but not just any people some very old friends one of which was thought dead

"hey Ran glad to see you're ok"

"Shinichi, it's good to see you too"

"um hey guys, been a while"

the FBI agents heard a fairly recognizable voice and are shocked to see Shuichi alive, burned but alive

"Shuu but how?"

"easy we faked my death, and ever since I've been in hiding I could never reveal myself to anyone who called out to me lest I put them, myself and our inside person in danger"

"good point well I have some news from our inside person that can only stay in Japan for now"

"what is it?"

"apparently the Black Organization has been forced to deal with a ghost stealing from them"

"a ghost?"

"yes a ghost"

"well what do they steal?"

"oh food, clothing, water, blankets, things that are needed for survival"

Shinichi quickly has an idea of who it was but needs confirmation

"this ghost wouldn't happen to be a phantom or more commonly called a kaitou now would they?"

"however did you guess?"

"wait but I thought he was killed five years ago"

"apparently he wasn't"

"looks like we're going to have to join him soon enough"

"true though I don't think he would approve of that"

"true but it's better than dying"

"speaking of Shuichi you have some explaining to do later"

"don't worry our inside person should be able to clear everything up once we can get in contact with them again"

well they start making joint plans though Ran's group decided to move to Agase's house next door unfortunately for them every plan they made to fight the Black Organization was counteracted and what was more was that the inside person was almost killed when the Black Organization found out Akai Shuichi was still alive so she had to fake her death to escape which meant they no longer had any inside information on them

"ok so we have no inside information and what's more we're all pretty injured from our last battle"

"plus our inside person is still hovering between life and death"

"any news from Kaito Kid?"

"none though we do know he's alive he's just not making any contact with us"

well for five more years they slowly start taking down the Black Organization, not in Japan, it would never be in Japan, but in places like England where Hakuba was or America where over half the Black Organization taskforce was due to letting themselves get captured there were resistances that rose up and defeated them but finally after five years all of the Black Organization taskforce and quite a few others had managed to sneak in and they were able to take down the Black Organization, but not without a price, Shinichi one of three people who had to hide from them wound up in a coma during the battle. Two years later in a hospital

"Shinichi when will you wake up?"

Hattori and Haibara walk in

"still no change?"

"none, the doctors state he's stable but that's about it"

well Kaito and Aoko also walk in Kaito being a reformed thief and now husband to Aoko to check up on him

"so how's tantei-kun?"

"no change"

"man it's been two years to the day and he still hasn't woken up"

"oh it is isn't it?"

"you haven't noticed the celebration that everyone outside is holding plus I heard the hospital staff is also holding a small party in honor of the two year anniversary"

"yes but it's simply some cake and soft drinks"

"so how does it feel to be free for two years Haibara-san?"

"it feels great I finally have a cure and I'm using my scientific skills for good"

"oh?"

"yes I'm now with the crime scene investigators that due analysis on any and all evidence"

"ah so you still see a lot of Takagi-keiji, Sato-Keiji and Nakamori-keibu then"

"yes I do see them a lot and also Shiratori-Keiji as well, in fact I'm the only person they trust the evidence too"

"what about the rest of the detective boys?"

"last I heard they're in college"

"what about all the school they missed?"

"underground schools remember?"

"oh yeah plus they also got the equivalent of the American GED didn't they?"

"yes"

"well then at least they're studying hard and doing good"

"I heard they might visit Kudo-kun at some point seeing as how they know his identity"

"that would be nice actually"

well Ran finally has to get up to stretch her legs but for some reason she can't and when she looks down she sees Shinichi holding her hand very tightly

"Shinichi are you awake?"

there's no reply but Ran is still more hopeful then she had been for the past two years. Three weeks later Shinichi finally woke up

"Ran where am I?"

"you're in the hospital Shinichi"

"why am I here?"

the doctor comes in

"Shinichi I understand you just woke up but what's the last thing you remember"

"going into a building to finally stop the Black Organization…no wait I vaguely remember searching for Gin and Vodka for some payback for what they put me through while on the second floor of the building but after that I'm drawing a blank"

"not surprising seeing as how you were hit from behind and then fell a floor to the ground, fortunately seeing as how a few others had seen you being ambushed they cushioned your fall and prevented potentially life threatening injuries"

"if I recall correctly Kaitou Kid decided to get some payback for that and after playing with them for a bit with hs new tricks knocked them out with his sleeping gas"

"well there doesn't seem to be any permanent damage however it's going to take you a long time to recover"

"I understand"

well for the next three months Shinichi went through physical therapy and was warned he had to continue to do so constantly so that he didn't risk ending up paralyzed and he did sometimes he got more than enough exercise chasing down criminals but at other times he had to do an hour or two of weight lifting and other specialized exercised though as he got older and had to retire he slowed down his exercise training and eventually did end up paralyzed but that was mainly when he was getting ready to die anyways