I'm here with another "R&D did it" blue
One of the R&D folks is the culprit and Solidus is the accomplice. The culprit leaves the platform by lowering the crane and climbing down, swim to another spot on the island where they have set up a rope earlier, and climb up. They can then return to the platform using the same path whenever someone goes there.
Mantis - Mantis entered the office, went to sleep, and got stabbed. The head bruise was inflicted posthumously.
Meryl - Culprit was outside the window, when Meryl entered (liquid just left and haven't gotten to the window yet) they throw the grenade in. Meryl then throws it out and dies. Culprit then dispose of it in the sea.
naomi - Culprit runs in front of the truck. The doctor then brakes suddenly (so they won't crash into them) and fly out of the car and through the window.
Solidus - Culprit set up the cactus in the shower and told their accomplice, Solidus, that they need to stab the cactus in their neck for superhuman power or smth (they're R&D so that's sorta believable?). Solidus does so and dies.
Gray Fox - Culprit, during the night, uses a grappling hook to get to the checkpoint blindspot from the water below. They then pour water/oil over that spot and uses a rope to climb back down (tugging the rope off the platform to get rid of it). When Gray Fox drive over the path he slips on the water/oil and loses control. Culprit burns the oil to get rid of the evidence/water dries before the others arrive.
Alternatively: If solidus wasn't the accomplice and died by other means i haven't identified, then the accomplice is Vulcan Raven who, on his dinner drive duty, paused at the blindspot to pour oil. He poured only a small amount so when Gray Fox drove there it got rid of most traces of the oil.
Ocelot - Culprit has a small tank of oil (technically explosive but there clearly were still oil on the island soooo). They light it on fire and roll it under the jeep as it drives by, causing it to explode.
Miller - Culprit convinced Miller to let him onto Tower 1 roof. They then told Miller to go onto Tower 2 roof. Culprit then use a long rope to lasso Miller and strangle him. They then hid on Tower 1 roof.
-=(blue)Liquid! You think your third rate theory will prevail against me, the one and only Furudo Erika? I will enlighten you on how this was done!
For Psycho Mantis' murder, the victim was lured to the boss' room. The culprit hid in the corner of the room, to the side of the entrance. Once Mantis entered he swing a large blunt object down onto his forehead head. Since he's coming from the side and Mantis is wearing the gas mask, thus limiting his peripheral vision, Mantis did not see the attack and is knocked out and murdered! The culprit then left, locked the door, then either threw the keycard into the room from either the roof or the restroom, landing on the desk.
For Meryl's murder, the nerve gas grenade was used. They threw it into the kitchen through the window, Meryl threw it back out then succumbed to the gas, then the culprit toss it into the ocean. The culprit wore Mantis' gas mask so they weren't affected.
For the Doctor's murder, either the jeep (and the warning lights) were tampered so the break wouldn't work and the doctor would fly out of the car and through the window, dying, or the culprit ran in front of the car, causing the Doctor to slam the break and fly out. You might say "but Multi everyone had an alibi!", and to that I'll say....
the culprit is one of the R and D staff! They left their platform by sneaking into the food delivery jeep then went back to the platform when Ocelot and Erika went back to check on them by sneaking onto their jeep!
Solid Snake - Culprit visits Solid, Solid approached cell bar, Culprit slams peg into Solid's skull and either the momentum sent them flying to the other side of the cell or Solid stumbled back and died there
Solidus Snake - Trap. I don't like it but I don't have a better explanation.
Gray Fox - Culprit was on the jeep. They tampered with it during the blindspot and leapt out after clearing the checkpoint.
Johnny, Ocelot, and big boss - All of their deaths can be explained if the weapons were retrieved - The culprit, after jumping out of the jeep and after everyone left, went down to the water with the help of his accomplice, the other R and D staff, and swam to where Erika disposed of the weapons. They then grabbed some of them, swam back to the R and D platform, and was lifted up by their accomplice. Weapons are thus acquired! They can then just leave the platform because the footage wasn't checked after that.
Miller - The culprit was on the roof with him. He strangled Miller and jumped off into the rose garden below. Maybe he survived, maybe he didn't.
And thus the events that have transpired are explained!=-
Each time someone left the inn (i.e. Bill to get check the lamp and Eiko and Gabriel to check on Bill) the culprit sneaked into the forest and screamed to attract their attention. The victim hears the scream, runs towards it, then gets nabbed by the culprit.
Bill is the culprit! He didn't actually went out to fix the lamp but ran off into the woods to carry out the plan. He's the only one who's familiar with the location (since he owns the inn) so he would've known about the cabin. Finn saw the fire and drove away in his car, hence the lack of a final unidentified body.=-
Beowulf's disappearance: The Ferris Wheel cabins actually have openable windows. Beowulf merely opened it, reach out, unlock the cabin, close the window, and escaped by climbing down the other Ferris Wheels.
Beowulf's murder/suicide: The blood trail inside Wolfgang's apartment was actually forced perspective. The culprit, after planting Beowulf's blood as trail in the hallway, painted some red dots on the lightbulb in the hallway such that, when it shines a light into the entrance of Wolfgang's apartment, the shadow would look vaguely like a blood trail. The culprit, Beowulf, then, while Wolfgang is distracted by Fenris, entered the apartment, substituted the forced perspective blood with real blood, chainlocked the door, and committed suicide.=-
Beowulf's disappearance: When Freki and Wolfgang were descending Beowulf's cabin, Freki, who knew how to operate the Ferris Wheel, distracted Wolfgang somehow and instead descended one of the cabin beside Beowulf's. Freki then, when controlling the cabins so the two can check every one of them, skipped one of the cabins (Beowulf's) while the two were distracted. Freki then later return, alone, after having a friendly walk in the forest with Wolfgang and the other dude and let Beowulf out.
Beowulf's murder: All of the reds regarding Wolfgang's apartment said "When Wolfgang left his apartment in the morning...", however the narrative made it pretty clear that he left it in the afternoon, at 1 PM. Thus the Reds do not apply and those theories can still be used. So, when Wolfgang left his apartment in the afternoon he probably left his window unlocked, or the culprit was hiding in there. Beowulf then entered via the window and got shanked. The culprit then hid in the room and ninja'd his way past Wolfgang and out of the room while Wolfgang was stunned by Fenris going full berserk on his apartment.=-
-=(blue)My body is ready.
Regarding the first mystery of Beowulf's disappearance, he had an accomplice (does not violate red since Beowulf is not the culprit). When he entered the ferris wheel cabin, while Wolfgang was making his way to the control panel (and thus wasn't looking at the ferris wheel), an accomplice came out of the bush somewhere, unlocked the cabin, let Beowulf out, and locked it up again. The two then escaped. Wolfgang didn't see that and assumed that Beowulf was still in the cabin as it ascend.
Earlier theories speculated that the apartment was across the river from the theme park so I'll use that too. Beowulf and accomplice crossed the river using a boat and arrive at Wolfgang's apartment.
The next question is how did they enter the locked apartment?
The answer; the diagram shown in the gameboard isn't merely the schematic of the apartment, it is a top down view of the apartment complex. That's right, Wolfgang's apartment's and the one above's ceilings were removed. This was likely done sometimes in the afternoon while Wolfgang was out.
Beowulf and his accomplice climbed the building side (accomplice helped Beowulf) and into Wolfgang's room. The accomplice then betrayed Beowulf, killed him, and planted a blood trail. (They unlocked the door from the inside and also planted the blood trail in the hallway. The masked guy Fenris saw in his footage is not relevant to the mystery.)
The culprit (who is called Luna because Luna's Trap) then climbed out the way they came in.=-
-=(blue)The culprit is Sir Charles.
The Engine in the case was a fake/replica. During the blackout the bottom flipped, sending the fake engine falling into the mechanism and bringing up the card, which was glued to the other side.
Since the engine was a fake Sir Charles didn't really care if it gets damaged by the mechanism inside the base.
Jorge was an accomplice. He planted the EMP rather than just disconnecting the fuse to make himself less suspicious.=-
-=(blue)It's the General.
The victim refused to meet the general and instead went to the roof (he left the room before 11.30). The general saw him and decided to sneakily follow him. Once on the roof, the general found the glass panel and discovered that the victim was actually the one behind the sun god messages.
He took this as a mockery of his superstitious believes, got angry, and stabbed him with an arrow he had.
To try and frame this as some sort of divine intervention, he carved the message into the arrow and pushed the victim down the hole into the living room. He then dropped the glass panel onto the victim before leaving.=-
-=(blue)The culprit is none other than the general! Midway through the conversation, the doctor led him to the roof, and told him about the glass panel trick.
Angered at the doctor's trick, the general stabbed him with an arrow he conveniently carried with him, killing him.
Panicked, the general decided to put a superstitious aura around the mystery to try and distance it away from himself. He wrote the words on the shaft, moved the glass into place, and put the corpse over the glass.
Due to the weight of the corpse, the glass would shatter given enough time.
The General then quickly left the roof and the compound. Some minutes later, the glass break, delivering the doctor's body to the living room.=-
-=(blue)Let's start with a simple blue.
The culprit is Sir Charles, with Jorge as an accomplice.
Sir Charles wanted the Argos Engine and didn't want to risk losing the case against the museum, so he impersonated Miss Mystery and hosted the gala. He paid Jorge off to help him with the crime.
The glass case was, infact, not chemically bonded, but locked with an electromagnetic lock (the glass reaches into a groove in the floor, and the electromagnetic lock is under there, holding the glass in place)
Charles had Jorge plant the EMP device when he was alone in the security room. When the EMP goes off, it blows the fuse, thus disabling the electromagnetic lock in addition to the lights.
During the chaos, Charles removed the now-movable glass, took the Argos Engine, placed the card there, then put the glass back. He then hid it somewhere on the venue, in a hidden compartment or maybe the male bathroom. After all, he's the owner of the property so there may be a hidden compartment only he knows about.
Once the light was fixed, the electromagnetic lock re-engages, making it immovable again.
Finally, he lied to Ito about the glass being chemically bonded.=-