Metal Gear is probably one of the most sound sagas in the world if you match the consistency of the continuity with its sheer depth and scope. You really have to dig to find a plot hole, and there are really only a few glaring issues that hardcore fans will notice. I will go through some of the biggest ones I’ve discovered.

First off, let’s get one thing straight: A common misconception is that the word «retcon» is equivalent to «plot hole» – only between installments. This is false. A retcon is a change in the continuity that DOESN’T mess with any pre-established fact. One that does is considered a plot hole. With that out of the way, let’s begin.

PLOT HOLE 1: The Nuclear Age

The opening of Metal Gear 2: Solid Snake makes the bold claim that pretty much all nukes in the world have been disarmed. This is why the threats of Outer Heaven and Zanzibar Land are so glaring during the 90s. However, in Metal Gear Solid – to mirror the real world – they establish the world as being more prone to nuclear terrorism after the end of the cold war.

SOLID SNAKE

«The nuclear age ended with the turn of the millennium.»

KENNETH BAKER

«No, you’re wrong. The threat of nuclear war isn’t gone. In fact, it’s greater than it’s ever been.» – Metal Gear Solid (1998)

What I find interesting about this exchange in MGS1 is that Snake is unaware of the danger of nuclear war in the new millennium. Which means that – while this whole thing may come off as a plot hole – Solid Snake is expressing the player’s view of this revelation. The player (or at least the two or three Japanese players who played Metal Gear 2 before MGS1) are probably thinking «but wasn’t the world free of nukes in the previous game?». That reaction from Solid Snake makes it apparent to me that the backstory in Metal Gear 2 might’ve been a cover story by the United States government.

However, we’re not finished yet … possibly. The most recent entry in the series, Metal Gear Solid V: The Phantom Pain, has an online feature that may tie into this old plot point – by way of the FOB missions. The way I see it: Venom Snake is disarming nukes around the world so that the nuke-free world that we see in Metal Gear 1 and 2 will exist and pave the way for Outer Heaven and later Zanzibar Land’s position as the world’s only nuclear power. Meaning that we’re going in a rectonny/plot-holey circle. Through this framework, the threat of nuclear terrorism is diminished at the end of MGSV to the point where Outer Heaven and Zanzibar Land pose a major threat. But as Kazuhira Miller says in the Nuclear Disarmament cutscene of MGSV (which may or may not be canon), the threat of other terrorist groups and nations rebuilding their nukes is still a possibility.

KAZUHIRA MILLER

«How long the world remains nuke-free is up to us. Will this moment persist? Or will human ambition cast us into the flames once more?»

– Metal Gear Solid V: The Phantom Pain (2015)

If we’re to assume that this scene is – in a sense – the «true ending» of MGSV, that means that at some point, the world becomes practically nuke-free, paving the way for Outer Heaven (which Venom Snake consciously works for, at this point) and its successor. But as made clear by Miller, there is no reason to assume that this status will persist. Especially considering that Diamond Dogs is disbanded no later than 1995. That gives the world plenty of time to secretly rebuild its nuclear arsenal.

To skip to my conclusion, the world remains mostly nuke-free from 1984 to 1999, but since MGS1 takes place in 2005, that gives the world plenty of time to rebuild its nukes.

PLOT HOLE 2: Solid Snake’s Father

The revelation in the first Metal Gear Solid that Big Boss is Solid Snake’s father isn’t necessarily a plot hole. He might as well be, you know. They were close, and Big Boss’ beard in Metal Gear 2: Solid Snake makes his face hard to make out anyway. The dialogue starts out fine.

SOLID SNAKE

«There was a man who said he was my father.»

NAOMI HUNTER

«Where is he?» SOLID SNAKE

«Dead. By my own hand.» COLONEL CAMPBELL

«Big Boss.» NAOMI HUNTER

«What?! Big Boss?! I had no idea!» – Metal Gear Solid (1998)

Judging from this, you can easily assume that Big Boss told Solid Snake this sometime before his betrayal in the original Metal Gear. But then Campbell says something that challenges this thought.

COLONEL CAMPBELL

«There’s no way you could. It happened in Zanzibar Land 6 years ago. Only Snake and I know the real truth of what happened there.» – Metal Gear Solid (1998)

This line is interesting, certainly. Not only does it imply that Big Boss and Solid Snake had a Luke-and-Darth-Vader-moment at the end of the Zanzibar Land disturbance, but it also seemingly breaks the fourth wall by claiming that the reason Naomi (and by extension the player) doesn’t know this is because only Snake and Campbell know the REAL truth of what happened at the end of Metal Gear 2 (which from a literal stand-point makes no sense considering the presence of Master Miller, George Kasler and Johan Jacobsen as Snake’s support team).

Personally, I think it’s just Campbell being unclear. When he says «it happened in Zanzibar Land 6 years ago», he’s probably talking about the death of Big Boss. And he likely doesn’t know that Miller was aware of Snake’s origins (seeing how he changed his bio between MGSV and MG2). My thoughts on this is that Snake was told about his relation to Big Boss shortly after joining FOXHOUND, which prompted him to receive his codename.

PLOT HOLE 3: Gurlukovich Mercenaries

A name dropped a number of times during the first Metal Gear Solid is the name Sergei Gurlukovich. He is described as the «head of Spetsnaz».

REVOLVER OCELOT

«The boss has a close friend high up in the Russian government. He’s currently the head of Spetsnaz.» – Metal Gear Solid (1998)

In Metal Gear Solid 2: Sons of Liberty, however, he is frequently referred to as the leader of a private military group of ex- Russian soldiers. The change in description is a little bit jarring to say the least. But there’s actually a very simple explanation: He’s both Spetsnaz and mercenary leader, as evidenced by this little exchange between Snake and Otacon.

SOLID SNAKE

«Gurlukovich… One of Ocelot’s allies.» OTACON

«Yeah. The GRU colonel.» – Metal Gear Solid 2: Sons of Liberty (2001)

I’m not an expert on how the Russian/Soviet military works/worked, but I know that GRU and Spetsnaz are closely related.

KGB SOLDIER

«You! You’re from the Ocelot unit of Spetsnaz! What’s a GRU soldier doing here?»

– Metal Gear Solid 3: Snake Eater (2004)

In retrospect, it’s weird to include this as a «plot hole», but since many get confused by it, it’s worth clearing up here.

PLOT HOLE 4: Liquid Ocelot’s Arm and Voice

Liquid Ocelot is established in Metal Gear Solid 2: Sons of Liberty as Liquid Snake taking over Revolver Ocelot’s body to carry out his own plans to kill his brothers and destroy The Patriots. At this point, we don’t know what Ocelot’s motives are, other than to carry out The Patriots’ plans.

Metal Gear Solid 3: Snake Eater also implies that the possessions might be related to Ocelot’s genetic ties to The Sorrow.

Metal Gear Solid 4: Guns of the Patriots, however, seemingly ignores all of these things by explaining Ocelot’s new personality as a mixture of hypno- and psychotherapy, and – of course – nanomachines. He is also revealed to be carrying a prosthetic arm instead of a transplant from Liquid Snake’s corpse.

My theory is that the possessions, the transplanted arm and the ties to The Sorrow are all true – but only in MGS2’s case. In MGS4, Ocelot gets rid of Liquid’s arm and replaces it with a prosthetic. You might say that Ocelot never did carry Liquid’s arm in the first place, but the contrary is made clear when Solidus Snake mentions participating in the funding of the transplant.

REVOLVER OCELOT

«This damn right arm…! Liquid! It’s almost as if it’s having its revenge!» SOLIDUS SNAKE

«How much do you think we spent on that arm in Lyon? The best transplant surgery team in the world.» – Metal Gear Solid 2: Sons of Liberty (2001)

In addition, Rosemary mentions Liquid Snake’s corpse (at the time thought to be Solid Snake’s, due to a cover-up by Philanthropy) missing an arm.

ROSEMARY

«The right arm was missing, but there’s no doubt that it was him. That body belongs to Solid Snake.» – Metal Gear Solid 2: Sons of Liberty (2001)

So now that we’ve established that Ocelot actually did wield Liquid’s arm, but ended up replacing it at some point between MGS2 and MGS4, the question becomes: Why would he want to replace the arm with a prosthetic? The only explanation is that Liquid’s possessions were real and getting in the way of Ocelot’s plans. This means that the belief that Liquid Snake’s last moments were during the Shadow Moses incident is likely a misconception. It’s only in MGS4 that Ocelot is pretending to be Liquid, which explains why we hear Liquid’s voice in MGS2 and Ocelot’s voice in MGS4.

Now then, why did Ocelot decide to recreate Liquid Snake’s persona after getting rid of the real thing? Big Boss explains at the end of MGS4 that Ocelot did it to fool The Patriots into thinking he was trying to take over their systems. Thus, they would use Solid Snake to help shut down GW with a virus in an attempt to disarm Liquid of his position in the system – not knowing Ocelot was planning to destroy the system with that same virus.

BIG BOSS

«And Ocelot, in order to fool the system, used nanomachines and psychotherapy to transplant Liquid’s personality onto his own. He used hypnotic suggestion to turn himself into Liquid’s mental doppelgänger.» – Metal Gear Solid 4: Guns of the Patriots (2008)

PLOT HOLE 5: Naomi Hunter’s New Accent

This is a point exclusive to the English version of the series. The real reason Naomi Hunter’s accent was changed was because – in her backstory – she was raised in America for most of her years. From that stand-point, her British accent in the first Metal Gear Solid makes little sense.

It’s worth noting that the change in accent was first made in Metal Gear Solid: The Twin Snakes, but Kojima has been quick to disown that game as a canonical update of the original – probably because of its numerous flaws in execution. In any case, how should we go about explaining Naomi’s change in accent?

I’m not sure why they decided to give her a British accent in the first place. Regardless – while I personally prefer her American accent – it’s become an iconic part of the series.

My guess is that she wanted to confuse the people around her. After all, she was willing to buy her identification while working against Solid Snake and The Patriots. Her change in accent in MGS4 might be a reflection of her coming to terms with her true self. Committing suicide at the end of the game is part of the plan, after all. And that too is a response to her own introspection (as harsh as that may sound).

By getting rid of her – presumably fake – British accent, she accepts who she is and goes on to erase her sins from the world.

PLOT HOLE 6: Raiden’s Commanding Officer

Summing up Raiden’s military career is one of the harder things to do when analyzing the Metal Gear canon. What’s clear is that he started off as a Liberian child soldier in George Sears’ Small Boy unit. Then he was saved by a human rights organization and brought to the United States. His memory of the experience was wiped by his own subconscious denial, and he was recruited by The Patriots for the S3 plan for that very reason.

During the mid-2000s, Raiden was VR trained to match the skills of Solid Snake. He was then introduced to an AI illusion of Colonel Campbell, posing as a commanding officer for the fake FOXHOUND unit Raiden was supposedly a part of. In other words, Campbell was never Raiden’s commanding officer. At least not before or during MGS2.

RAIDEN

«Colonel. I just remembered something.» THE PATRIOTS

«What?» RAIDEN

«That I’ve never met you in person. Not once.» THE PATRIOTS

«Hm…» – Metal Gear Solid 2: Sons of Liberty (2001)

But in MGS4, Rosemary – Raiden’s girlfriend and «military analyst» during the Big Shell incident – tells Solid Snake that Campbell WAS Raiden’s commanding officer.

ROSEMARY

«Roy was worried – he was Jack’s commanding officer. But Jack just avoided him.»

– Metal Gear Solid 4: Guns of the Patriots (2008)

Rosemary was a spy for The Patriots in MGS2, and was probably kept on a strict need-to-know basis. She likely never knew that the colonel was really The Patriots’ AI, as that was revealed to Raiden by Otacon after she had been detained by The Patriots.

As for Campbell, he was probably worried about Raiden on behalf of Snake, since the latter did feel a certain amount of guilt for Raiden’s recent trauma. Rose, still under the impression that Campbell too had been a puppet of The Patriots during the Big Shell incident, attributed that to their supposed relationship during said incident.

PLOT HOLE 7: Dr. Madnar’s Arc

Dr. Madnar is a prominent character in the two first Metal Gear games. In the first one, he plays a role similar to Otacon in MGS1 and Huey in Peace Walker, as he is forced to build a Metal Gear for Outer Heaven. In the second game, however, he pretends to be in the same position when he’s really working with Big Boss to take revenge on the West and their scientific community.

Near the end of Metal Gear 2: Solid Snake, Dr. Madnar attacks Solid Snake when he is caught having murdered his colleague, Dr. Kio Marv. He is eventually defeated. In his supposed last moments, he tells Snake how to destroy Metal Gear D.

But then – 15 years later – he returns off-screen to save Raiden from Vamp’s injuries in MGS4. There are a few false claims people make to call this a plot hole.

The first one is that Dr. Madnar «clearly» died in Metal Gear 2, even though he’s one of the few bosses in that game that doesn’t incinerate or explode (unlike Gray Fox and Big Boss, whose survival people seem more willing to accept). And his last dialogue comes long after he’s been pumped with several missiles during his boss fight.

It’s not really uncharacteristic either. Dr. Madnar could be seen as one of Snake’s few friends after FOXHOUND’s set-back with Big Boss’ betrayal. He obviously felt guilty about his own betrayal at the end of the game, and that might be why he’s willing to help in MGS4. It’s a little weird that Snake doesn’t raise an eyebrow when he hears Raiden speak the name, but maybe he’s REALLY put that past behind him.

PLOT HOLE 8: Para-Medic is Dr. Clark

Dr. Clark is established in the first Metal Gear Solid as the former chief of the medical staff at FOXHOUND. He is revealed to have been responsible for Gray Fox’s transformation into a cyborg, and that he died in the explosion from Fox’s escape.

Then, in Metal Gear Solid 4: Guns of the Patriots, it’s revealed by EVA that Para-Medic from Metal Gear Solid 3: Snake Eater and Dr. Clark are the same person.

EVA

«The project was led by Dr. Clark, known at the time as Para-Medic.» – Metal Gear Solid 4: Guns of the Patriots (2008)

But Naomi clearly referred to Clark in MGS1 using a male pronoun.

NAOMI HUNTER

«My predecessor, Dr. Clark, was in charge.» COLONEL CAMPBELL

«Dr. Clark?» NAOMI HUNTER

«Yes. He started the gene therapy project.» – Metal Gear Solid (1998)

Alright, so this is a bit of a plot hole. How can this be explained? Well, we wouldn’t get a truly canon explanation until 7 years later.

In a cassette tape between Venom Snake and Huey, the latter reveals some information he acquired about Dr. Clark during his time with XOF.

HUEY

«This Dr. Clark is a complete ghost – even to others in his field. His age, where he comes from… That might not be his real name. And I can’t even say for sure if he’s a he.» – Metal Gear Solid V: The Phantom Pain (2015)

This little dialogue is a clever piece of plot hole-filling. For so long, fans have complained about the inconsistency in Clark’s gendering, and now we finally have an explanation for that too.

Even to others in her field (that would include Naomi Hunter), Dr. Clark was a ghost who kept to herself and left any hint of her identity unknown. She probably delivered her orders through proxy, which makes sense considering how closely affiliated she was with Zero and The Patriots.

PLOT HOLE 9: Mei Ling’s New Accent

Just like Naomi Hunter, Mei Ling is another returning character in Metal Gear Solid 4: Guns of the Patriots whose voice actor was kept but whose accent was completely changed. In the original Metal Gear Solid, she has a Chinese accent. In MGS4, she has an American accent.

The real-life explanation is the same as with Naomi: Mei Ling was raised in America, and thus it makes more sense for her to have an American accent. But then again, she mentions being raised in Chinatown, where most people speak Chinese instead of English. Since she’s only 19 years old in MGS1, it’s logical for her not to have grown out of her accent just yet.

Her cameo in Metal Gear Solid 2: Sons of Liberty retains her Chinese accent, but it’s slightly clearer now. Or that might just be my wishful thinking.

Finally in MGS4 – at an age of 28 – it’s pretty logical for her to have gained a fluid American accent. Especially with her new position as captain of the Missouri.

And yes, I know Mei Ling’s accent was first changed in Metal Gear Solid: The Twin Snakes. But that game isn’t canon, so it really doesn’t prove anything.

PLOT HOLE 10: Bay of Pigs

This is not really a plot hole – again. But it’s somewhat jarring.

Prior to the final battle with The Boss in Metal Gear Solid 3: Snake Eater, she explains that she went underground as a result of her participation in the Bay of Pigs operation, as she felt betrayed by her government.

THE BOSS

«In 1961, I was sent to Cuba – to Bahía de Cochinos. It was part of a CIA-sponsered invasion under the guise of taking Cuban exiles back to their country. But the US government betrayed them. Our weak-kneed president held back their air support. Defenseless, the exiles were annihilated by the Cuban army. All I could do was watch in silence. I was set up by the very country I’d sacrificed so much for; by the very government I’d dedicated my life to defending. I was driven from the surface world, and I went underground.» – Metal Gear Solid 3: Snake Eater (2004)

In the fifth chapter of Metal Gear Solid: Peace Walker, you can listen to tapes from EVA detailing The Boss’ career prior to the events of Metal Gear Solid 3: Snake Eater. In one of the tapes, EVA explains that – due to the Mercury Project’s failure during the space race between the US and the Soviets – The Boss’ accomplishments during that mission were erased in place of a cover story: Her participation in the Bay of Pigs invasion.

EVA

«Not only did they expunge her flight from the records, they denied that she ever existed. And that wasn’t the end of it. As an alibi, the military claimed she’d taken part in the CIA’s botched Bay of Pigs plot to take back Cuba.» – Metal Gear Solid: Peace Walker (2010)

Why would The Boss use this non-existent experience as an example of the government setting her up – to her most trusted apprentice, no less?

One simple explanation is that – because she was still under orders from the US – she might’ve wanted to keep the government’s narrative in place. After all, she had already entrusted EVA to tell Big Boss the truth anyway.

A slightly more philosophical explanation would be that to her, the incident – even if she wasn’t directly involved in it – was still a betrayal. Not only were her true efforts covered up in favor of a botched invasion, but the invasion itself convinced her of her government’s lack of empathy. After all, she wasn’t there to help the Cuban exiles, so all she could do was watch in silence.

PLOT HOLE 11: Cipher

Metal Gear Solid: Peace Walker’s disconnect from the rest of the lore is seemingly apparent right until the end, when it’s revealed that Paz is working for Zero’s organization: Not The Patriots, but Cipher.

PAZ

«My entire life has but one purpose: To carry out Cipher’s plan!» – Metal Gear Solid: Peace Walker (2010)

EVA’s explanation of The Patriots’ origins in MGS4 seemed to suggest that The Patriots had been their name since its conception; nothing seemed to suggest that the organization was named something else. The logical thing to draw from this retcon is to assume that Cipher was the original name of The Patriots, but that’s not entirely certain either. In a cassette tape acquired after the final boss in Peace Walker, it is implied that Big Boss is unaware of the name Cipher, even though he’s a former member of whatever The Patriots were before 1972.

BIG BOSS

«Cipher… Ring any bells, Kaz?» KAZUHIRA MILLER

«Cipher… Cipher… It means code. Or zero in Arabic numerals.» BIG BOSS

«Zero…» KAZUHIRA MILLER

«Does that mean something to you?» BIG BOSS

«Not sure.» – Metal Gear Solid: Peace Walker (2010)

The next thing you may assume is that the organization was originally named The Patriots, but changed its name to Cipher after Big Boss left, and then later back to The Patriots – maybe when they re-aquired Big Boss after the fall of Zanzibar Land. After all, the word cipher means hollow or empty, and Zero did feel empty without Big Boss at his side.

This reading has been contradicted with the release of Metal Gear Solid V: The Phantom Pain, however. In one of the Truth Tapes, Ocelot makes it very clear that The Patriots is a name that came a few years after the fall of Militaires Sans Frontièrs. It served not only as Zero’s rebranding due to Skull Face taking control of Cipher through XOF, but also as the collective name of the AIs being developed by Donald Anderson.

REVOLVER OCELOT

«Oh, and they’ve got a name for Anderson’s AI project: It’s called The Patriots.» – Metal Gear Solid V: The Phantom Pain (2015)

So, the only assumption left is either that Cipher was the organization’s original title and Big Boss just wanted to forget about it, or that it was called something else before 1972. I doubt the former is true, since the name Cipher refers to Zero, and he wouldn’t be so narcissistic before Big Boss left him.

PLOT HOLE 12: Big Boss Was in His Late Fifties

This one is pretty glaring. In Metal Gear Solid 2: Sons of Liberty, Liquid Snake (AKA Liquid Ocelot) tells Solid Snake that the reason his body is decaying so rapidly is due to Big Boss being cloned at a late age.

LIQUID SNAKE

«Our raw materials are vintage, brother. Big Boss was in his late fifties when they created his copies.» – Metal Gear Solid 2: Sons of Liberty (2001)

This whole statement has been contradicted later in so many ways, mainly through the revelation of Big Boss’ date of birth.

My explanation is simple: Liquid Snake has gone mad, and/or is trying to intimidate Snake with misinformation. I would say that Liquid has a tendency to make very bold assumptions, and it doesn’t help that he was probably being fed lies by Revolver Ocelot during the Shadow Moses incident. But considering that Metal Gear Solid V: The Phantom Pain shows him actually meeting Big Boss (or at least thinking that he does), I can say bye-bye to that argument (thanks to Dennis Bosmans for contributing to this part).

PLOT HOLE 13: Gray Fox in Vietnam

Gray Fox’s backstory is probably the most contradictory aspect you’ll find between Hideo Kojima’s canon and the expanded universe. But ignoring that for a second…

In Metal Gear 2: Solid Snake, Gray Fox reveals that he was first rescued by Big Boss from a Vietnam half-white concentration camp after the war (meaning probably around 1975).

GRAY FOX

«I was a half-white living in Vietnam… It was after the war, and half-whites were being sent into forced labor camps. He saved me from that living hell.» – Metal Gear 2: Solid Snake (1990)

But in Metal Gear Solid V: Ground Zeroes – and by extension The Phantom Pain – we are told that Big Boss was in a coma from 1975 to 1984.

Only two explanations remain: Either Gray Fox had heard the legends about Big Boss, and hallucinated a scenario in which he was saved by the legend himself. Or he was rescued sometime after Big Boss’ awakening, though I have a hard time believing he’d survive being kept in a forced labor camp for 9 years – or that such a camp would even exist so long after the fact (I haven’t read up on it though, so I might be wrong).

This is probably the biggest plot hole in the series, assuming my observations are correct. I would reframe Fox’s backstory in Metal Gear 2 as proof that he’s been delusional since his early days, and it can stand as an example of how Big Boss affects other soldiers even while he «sleeps».

So that was all the plot holes I could fill. I mean, there are some other minor ones that I can dissect – and I’d love to hear suggestions – but I think that’s enough for now. Take care.