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You only can play as character pertaining towards their role in the game? Or can you freely choose them
You just play them on chapters only so that means no free mode for other characters.
Same as in story.
You can choose between 9S or 2B (if either will follow you when you're the other person) between ending A and B but after ending B you can choose A2 or 9S after you earn the achievement that makes you watch 2B die (wonder what happens if you choose 9S...)
How does level impact chapter. Say we are level 99, but we want to restart the game from the 1st chapter while still having a healthy amount of difficulty

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Unfortunately, level 99 in chapter 1, part A is only going to be challenging on "Very hard". You get oneshotted by any hits on "Very hard". But most people would prefer enemies that scale to your level instead of turning the game into a oneshot or be oneshotted fest.
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Fallenangel700

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At that point, it might be better to just make a new save file and start over. Unless you want to do what Chaosmaker suggested and put it on very hard.
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You can also do that. Once you finish the game a third time (Endings C/D/E) you just have to save (don't erase your data) and you will be at the very beginning of the game with enemies up to your level (you keep the Chapter Select function)
The game is very level and stat dependent. Fighting Eve for instance while you are level 1 will deal 0 damage to him no matter which chips or weapons you have. Starting the game over at level 99 with all weapons and chips is just pointless. You one shot everything. I tried resetting my level to 1 and using only bare fists on hard mode, but it was still to easy because 9s had weapons equipped from the previous playthrough. It's actually more fun to just delete a save game and start over completely.
Will i be able to replay older chapters to get weapons i missed out on?
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Fallenangel700

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Yep. You unlock a chapter select function after the third playthrough.
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Yea
Can sidequests be reset?
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Someone please correct me if I am wrong, but side quests cannot be reset. However, the side quests that went unfinished or were not started yet may be played through later by employing chapter select. An option then, may be to play through only the main story line (no side quests) to the point after endings A and B and then save your progress to that point as a permanent way to play the game from any point forward with all side quests still playable. (This should stay viable if the A + B completed game without any side quest play is always re-saved again in an alternate slot before any further game progress is made when playing again from chapter select.)
No they don't. Nothing resets except for main story line. This is a real downer.
Is it possible to change character in Debug Room? How come it gives me 9S to practice?
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Fallenangel700

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The one time I used it, it gave me A2. Maybe it's the last character you used?
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It's always the last character you used.
Will golden machines will appear in Route A, B, or C?
Golden machines appeared in Route A and B for me so far, can't say for C as I'm not there yet.
Why does 2B and 9S voices sound high pitch and distorted?? It happened after k finished the 3rd play through and got the D ending. Is there a way I can change it back?
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Fallenangel700

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Never heard of that. I can't think of any reason they would be like that, so maybe it's a glitch?
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you can change the voice pitch after beating the game one. I've did it before, you can change it back to default. Maybe this will help
System : Settings : Other : Voice Changer. Normal is 5. Other settings will distort the voice.
wait, let me get this straight. if you dont do anything but the storyline then you'll be able to replay them again and again once new game plus kicks in? Or is this only because you made a save file that only did the main quest and just keep rebooting from that?
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Once you beat ether ending C or D, you unlock chapter select which lets you jump to any part of the story as many times you want.
Slayer of Demons,Inquisitor,Ylissean Tactician,Kindred Hunter,Gray Warden,Dark Lord,Good Hunter,Chosen Undead,Nerevarine,Exile,Mugunghwa Investigator,Tremere Anarch,ESPer,Squad 7 Hero,Nohrian Prince,Arisen,God Eater,YoRHa Android,Tenno,Hope's Peak Dropout
Worst implementation of a new game plus ever. Learn from Tales games.
Or the Souls/Borne series. I agree a new game plus should be a new game experience with more difficulty and what not, but the game is really well done overall, so I think a new game plus adding so much more is asking for too much from something that's already complete.
shut up *****, this game is amazing and you're a ***** kid. kys