Hello all!
I would like to say I had a great time with this game, honestly it's not what I expected and I was very pleasantly surprised, then brutally crushed with the endscene. Though it is likely most chatter and suggestions here would be mostly ignored or only glanced at, I thought I would at least put out my suggestions somewhere where they might be seen.
I may prattle on for a little bit, so brace yourself if your willing to go through it, and I'm happy (and even eager) to hear anyones thoughts in reply, or even 'improvements' on my own!
First up, I have to say that I'm in the 'denial' boat, though I don't doubt there are a whole bunch of others out there, as I mentioned, I got pretty emotional at Lee's 'death' scene, but it was left a little open. I played through it twice, the second time to see what the different options effected, but both times I had Clem shoot Lee at the end.
Though Clem did point the gun at Lee,, she closed her eyes, pulled up the gun and fired, but then Lee gave a quick faded laugh in the blackout. This would suggest either that Clem couldn't actually shoot Lee, missed entirely, or hit him in the body leaving him to be reanimated. In the first case, perhaps the bullet grazed Lee's head, and he blacked out? It could have missed entirely, or entered in a non-fatal area.
But I hear you say, "So what if he didn't die to the shot? He was infected! Whether she missed or not, Lee's gone. Zombified or otherwise!" (or "That 'laugh' was just some zombie in the background! Don't be silly.(<--- what?! Heresy! D: )) Well, I'm here for suggestions, not simply to debate whether she shot him or not!
So, for my desperate but futile attempt at keeping the Clem and Lee team going, here's my suggestion and ideas: One way, Lee is shot, the other I believe he is left there by Clem to turn, because he doesn't want Clem to go through killing him. (bear with me here, till you hear all of the suggestion, it may not make sense till you hear its completion)
(This may also depend on whether you told Clem to 'trust no-one' or to go with Omid and Christa, the other option(s) would be the same as if you told her to go with Omid and Christa. Though its not necessary, it's a thought on the previous series last conversation and action/reaction)
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In the first case; Clem would have missed, either grazing his face giving him a scar, or couldn't bring herself to kill Lee. She couldn't just abandon him there either, so she stays, crying into his chest. Omid and Christa come back looking for Lee (regardless of his wish, ie if you told them to go to the train) and find Clementine sleeping on the very pale, walker-blood spattered lee, still cuffed to the radiator(?). Scene Blackout.
In the second case, where Clem leaves Lee; Either Clementine would meet up with Omid and Christa, who go back for Lee (for whatever reasoning, to finish him off, perhaps, maybe Clem demands they bury him). They agree and return when it quietens down.
(OR, if you had chosen not to trust anyone AND to spare Lee, Clementine decides to go back on her own because she feels horribly guilty)
Clementine(+ Omid and Christa(if selected)) enter the back cautiously and see Lee's cuffed to the radiator, pale, and still breathing! Everyone knows he should be long dead and turned, so what's going on? Scene blackout.
Lee wakes up in a strange new environment (With the obviously assosciated heavily blurred vision), with the voice of Clementine 'guiding' him back. He tries to sit up, but is still very weak, and tied down onto a bed. It is now that Omid and Christa chime in, telling Clem to get back, be careful, because they dont know if he really has turned or not. Lee is slightly less pale now, but still appears very ill. Scene blackout
He wakes up again to see Clem sleeping on a mattress nearby, and wakes her to begin a dialogue. Dialogue can be worked out in time, but it would end up with Clem or Lee shouting out he's awake, Omid and Christa come in and join the conversation. (If Clementine was the only one to come back for you originally, Omid and Christa explain that they came back for you (regardless of your wish) and they saw Clementine trying to drag you away, so they came to help.
They all ask him how he could possibly have survived. In the case of your arm being cut off, that's what it would be associated to in the beginning. If you chose not to cut your arm off, the only explanation is that somehow your body became immune to whatever infection the 'walkers' give through blood transmission.
You spend a little time around their temporary house, obviously very weak still. When done at the house you gather back together and decide whether you should split up or stay together, Clem, depending on what you said(trust noone, go with Omid/Christa, neutral) wants the specific thing. (The whole"clem will remember this" thing) Then it returns to a cinematic, back to where the previous series left off, with Clem looking at figures in the distance, and looking at her gun, only now Lee(,Omid and Christa, if you chose they should come) come up, with Lee putting his hand on Clem's shoulder, appearing less pale, but still weakened.
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In addition to this 'saving' of The Lee and Clem team, there would be either an episode, or a major part, focused on trying to get Lee's blood to some facility as some sort of 'cure', likely ending in the facilities destruction.
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For people that had their arm cut off, it would add like a slightly separate conversation line through the series, perhaps people letting you off a little easier, certain cut scenes being a little different, and those with their whole arm would have more trouble with strangers, because the bite mark would still be visible on his arm. Though he'd cover it, he'd inevitably get found out by strangers. (I dont know the storyline planned for the next season).
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Though desperate I am, I would not accept the "It was a dream" scenario, where he dreamt whatever part of his troubles, and neither would anybody else. I don't think the team would even consider it, but either way, no dream.
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I also understand that for people who didn't play Season 1, they would need something to go off of if they play 2 without playing 1 first. In this case, I believe it would be dealt with in one of two;
A sort of innocent 'quizz' or 'questionarre' at the start, asking the player what they would do, if it was them in a zombie apocalypse, and sneak in as best you can the questions of cutting off your arm, would you take from some random car etc.
Letting the player choose. Randomising it would only really work if they player was happy with however it started out, ie, if they wanted to have both arms, yet it was cut off, they would continue to randomise games until they got his arm back. Some may even want his arm still cut, for the experience of different dialogue, story or experiences.
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I would like to point out that a long 'Timeskip' may not be the best option either. Clementine has been a character already moulded, and she has her own personality already, supported by lee in the past, the same goes with Omid and Christa. It may also conflict with the ongoing series, but I'm not sure of the ramifications of that. One way or another I believe they would include Clementine, however, it should certainly not be an 'older, controllable her'
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Though peoples ideas may or may not be good, and I'm sure people would have mixed feelings about my suggestions, I'm fairly sure season 2 would be pretty damn hard to manage, code and storywise if it was a continuation of series 1, but it is certainly very much what I would like, though I'm not sure about the majority of others.
Don't get me wrong, I've seen people say they want an entirely new story, and while I would still play a new arc, I would very much miss the ultimate duo that is Clementine and Lee. It would also give developers a chance to REALLY have a play with everything that you chose to tell, teach and show Clementine and see how it works out in series 2. IE, if you killed one or both of the brothers (Andy/Danny), she ends up shooting some random stranger even if you tell her not to, steals from others if you chose to take from the van, the team could have a great play around with consequences.
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I realise Telltale have their own teams, writers, storboarders etc and will more than likely want to portray their own story in their own way, maybe even a completely new and different story arc, but perhaps they just might get an idea or two from the public and implement it somewhere, or if its good enough, have a main part revolving around it in a different perspective. (Or, hopefully save Clem and Lee

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I may have some grammatical errors or a plothole here that I haven't noticed, please do say something >.<