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At the end of Metroid Prime

We find Metroid Prime in the crater where the Phazon meteor struck, equipped with many weapons stolen from the space pirates.

We can see in several places that the Space Pirates were unable to enter the crater's interior, though they knew something was in there.

Impact Crater
Log 11.156.9
Investigations into a possible ingress point for the impact crater continue to meet with failure. The shield of strange energy that protects it is impermeable, and all attempts to tunnel past it have proved fruitless. Our continued futility in this matter is made all the more significant in light of the recent life form readings we've discovered emanating from deep within the crater. Analysis of the readings indicates that a massive creature is gestating there, absorbing enormous amounts of Phazon from the Phazon core at the heart of the impact crater. This discovery makes accessing the crater doubly important - not only will it open the door to the vast deposits of Phazon within, but it will also lead us to this creature, whatever it may be."

Later, we discover that the Space Pirates understand the artifacts, but have not found them yet. When Samus enters the impact crater, it is only after she finds all 12 keys.

The Key
Log 11.452.8
Although we are no closer to finding the artifacts of the Chozo, we have at least produced a viable hypothesis for their function. It appears that each of the artifacts corresponds to one of the statues on the temple platform, and that each one acts as a small key to a huge lock. Judging by the number of statues, we assume there must be twelve artifacts. Once we find the resting spots of all twelve, we can bring them here, unite them with their statues, and open the gate system at long last. Once we do, the impact crater - and whatever creature it shelters - will be ours for the taking."

Yet, there are additional logs that detail Metroid Prime's arsenal and armor

Metroid Prime
Log 11.156.9
Test subject Z-d, hereafter referred to as Metroid Prime, was recently discovered in a cavern by mining crews. It quickly dispatched the miners, but was eventually contained by security units and drones. Once contained, we were able to begin studies upon Metroid Prime

Prime Breach
Log 11.377.1
Subject Metroid Prime's breach has been contained. Reports indicate that it sensed a large batch of raw Phazon in the lab from within its stasis tank and broke through the glass, using previously unsuspected strength. Besides consuming all of the Phazon, Metroid Prime assimilated several weapons and defense systems from fallen security units. It has suffered no ill effect from said assimilation: indeed, it began to use its newly acquired weapons against us. Once we pacified it, we were unable to remove the assimilated gear without threat to Metroid Prime — the gear is now an integral part of its body. Command is intrigued by this newfound ability, and has ordered further study to commence at once."

Here it notes that a few of the logs I've quoted here were ONLY in the original North American version.

So, how did the Space Pirates get into the crater, or is there an actual contradiction that caused the retcon?

  • Not sure I understand the question. Metroid Prime, aka "The Worm", was originally sealed inside the temple by the Chozo, which is a major point of the plot. Did you mean something else? – Omegacron Dec 30 '14 at 14:16
  • Reading here, it says that they were never able to enter the crater. It also says that they were able to study metroid prime and even contain it. Almost all of metroid prime's weaponry and armor comes from technology assimilated from them. It also notes that that the entries that talk about metroid prime's holding and the study of her was only in the original NA version, so perhaps it was retconned? – Premier Bromanov Dec 30 '14 at 20:05
  • Ah, ok. So the actual question should be "How did the pirates gain access to Metroid Prime?". The Metroid Prime life-form itself - which later becomes Dark Samus - was inside the meteor when it originally crashed. The Chozo built the temple, artifacts, and seal to keep it from getting out of the crater. The Phaezon suit allowed Samus to pass through the seal, so I'd imagine the pirates had access to similar technology. – Omegacron Dec 30 '14 at 20:08
  • ahh, right, i was thinking backwards yesterday. Similar technology or no, the space pirates were never able to enter the crater because they couldn't find the keys. Samus was able BECAUSE she found all the keys. – Premier Bromanov Dec 30 '14 at 20:18
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    Reading all the logs, it seems to me that there's a big inconsistency here. The game goes to great lengths to conceal what's in the crater, yet in the North American version, there are logs indicating that it broke free, stole tech, and somehow ended up getting back inside the "impenetrable" forcefield. I'd chalk this one up to the NA version adding in unnecessary and contradictory lore. – user44330 Apr 22 '15 at 19:28
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Yes, it's a plot hole which was fixed in later releases, but which created another plot hole.

First of all, your question is more than a little confusing, because it apparently quotes two logs from the first version of the game, the NTSC (North American) version, and two from the updated PAL version. (Notably, the NTSC version was released before the Japanese version, and the latter also changes the story in accordance with the PAL version.) So to support your question you quote two different, and contradictory, plots, which is fine because you're asking about this contradiction – but you don't quote the entirety of either of the plots, which is a little confusing.

The first and second logs you quote, log 11.156.9 "Impact Crater" and log 11.452.8 "The Key", are from the updated PAL version. The other two, log 11.156.9 "Metroid Prime" and log 11.377.1 "Prime Breach", are from the first NTSC version. (You also quote the two different versions of one of the logs, log 11.156.9.) Since you're asking about the plot hole in the NTSC version, here's the version of the second log you quote from that version:

Chozo Artifacts
Log 11.452.8
We are particularly interested in a number of curious Chozo Artifacts we have been able to recover from a number of religious sites on Tallon IV. These relics resonate with power, and yet we are unable to harness them in any way. Science Team is attempting to fuse them together with Phazon, believing that a link might exist between them. We know that these Artifacts are linked to the Chozo Temple that block full access to the Impact Crater. We have yet to crack this enigma, however. Command grows impatient regarding this matter: results must be produced soon.

In addition, here's one NTSC log you don't quote at all:

Prime Mutations
Log 11.402.5
Metroid Prime continues to feed and grow ever larger in the impact crater caves. Its hunger knows no bounds, and it has begun to manifest unusual mutations since its breach. These include armor plating on its epidermis and mechanical outgrowths that generate defense screens. These screens render it invulnerable to most weapon systems, but a flaw in the mutation leads to increased vulnerability to certain weapons. It compensates for this by shifting the screens quickly. This latest development concerns Security units greatly: they feel it's a matter of time before Metroid Prime corrects this defect and renders itself invulnerable to all weaponry. Containment would be nigh impossible if this were to occur.

As you surmise, there's a contradiction in the original NTSC (North American) version of the game. If we put together the logs from that version in chronological order by the log numbers – log 11.156.9 "Metroid Prime", log 11.377.1 "Prime Breach", log 11.402.5 "Prime Mutations" and log 11.452.8 "Chozo Artifacts" – the original story goes a little like this:

The Space Pirates, during their Phazon mining on Tallon IV, found Metroid Prime in a cavern, which is either the Impact Crater itself or adjoining caves that it had escaped into. It was a Metroid which was extremely adaptive to Phazon, and they watched it evolve rapidly, developing defensive armor plating. During one of its break-out attempts it adapted an ability called "assimilation" which allowed it to absorb and attach Space Pirate tech and armor to its body; technology it still possesses in both versions of the game when Samus fights it.

This assimilation is also the ability it uses when it steals the phazon suit from Samus and fuses with it in a last ditch effort to survive, thus becoming Dark Samus, which also happens in both versions.

In addition, the Space Pirates manage to find several of the Chozo Artifacts that unlock the Impact Crater, but they fail to discover their use.

The problems with this story:

As you found out, the issue here is that Metroid Prime is fought inside the Impact Crater. Nobody, including the Space Pirates, managed to enter the crater since the Chozo force field was erected, until Samus Aran unlocked it and entered herself.

Another issue is that in both versions of the game, Samus finds all the Chozo Artifacts in their original locations where they were hidden by the Chozo, and use them to unlock the impenetrable Impact Crater where she fights Metroid Prime. None of them are in the Space Pirates' possession.

The retconned story, and the issue it raises:

This was recognized as a plot hole by Retro Studios, who retconned it in the PAL version by removing all the references to Metroid Prime in the Space Pirates' logs. The new version of one of the logs you quoted as well as the one I quoted above are as follows:

Gate System
Log 11.377.1
Analysis continues on these accursed ruins and the Chozo temple that hovers near them. We are now completely certain that the containment field denying us access to the impact crater is linked to strange artifacts that belong in the temple... but we are no closer to finding them or deciphering the riddles that seem to cover every wall of this ruined place. Command grows increasingly anxious for a resolution to this matter, so we must redouble our efforts. X-ray squadrons will begin terrain sweeps within days - until they begin, patrols are instructed to report any and all architectural anomalies to their commanders.

Artifact
Log 11.402.5
We have come to another dead end. It is clear now that we will never discover the locations of the Chozo's artifacts until we can decipher the messages carved into the statues in this abominable temple. Our language databases are woefully inadequate, and our linguistic analysts can come up with little more than vague theories. The best hypothesis we can offer is that finding the artifacts will require items spiritually linked to the Chozo civilization. However, without these items, we are lost, and Command grows more impatient by the day. Results must be produced soon.

Putting these logs in chronological order as well, together with the PAL logs you quoted – log 11.156.9 "Impact Crater", log 11.402.5 "Gate System", log 11.402.5 "Artifact" and log 11.452.8 "The Key" – we see that the new story unfolds like this:

The Space Pirates find the Impact Crater, but are unable to breach it. They realize that mysterious Chozo Artifacts hold the key to unlocking it, but never find any of them. From power readings, they recognize a massive creature residing within

This retconned version of the story makes much more sense in-universe, solves both issues I mentioned above, and was also carried forward to the Nintendo Wii version of Metroid Prime, and is considered the canon story. So the answer to your question is that yes, this is a plot hole, which was retconned and fixed and is not really an issue anymore.

This retcon caused another contradiction, however, which the astute reader will already have recognized. When Samus reaches the inside of the crater and fights Metroid Prime, it's still in possession of Space Pirate technology. Where did that come from in this version of the story, where it never meets the Space Pirates?

There are a couple of possible explanations to this new plot hole later in the series.

It's obvious when you fight Metroid Prime in Metroid Prime that the initial intention was that Metroid Prime had assimilated Space Pirate technology, as chronicled in the NTSC version's logs. However, in Metroid Prime 3, Samus finds discarded pieces of armor that look like Metroid Prime's armor on Phaaze, the planet that is the source of Phazon. Perhaps its resemblance to Space Pirate technology is just coincidental, or perhaps the Space Pirates originally discovered this Phazon tech and "pirated" it on some other world. Or, perhaps not:

In Metroid Prime 3 it's also revealed that Phazon is more than just a highly radioactive mutagen: It's a giant, galaxy-spanning consciousness, and Phaaze itself is a sentient planet that seeds the galaxy with Phazon to expand its reach. Perhaps the Phazon encountered Space Pirates somewhere else than on Tallon IV and assimilated their technology, which made it available to all the different strains/seeds of Phazon on other worlds, including Tallon IV?

Since Samus finds what looks like a Metroid Prime husk on Phaaze, as mentioned, one implication could be that it's not a Metroid at all, but that it came from Phaaze. However, another log entry ("Leviathan Infant") from Metroid Prime 3 offers an alternative explanation for Metroid Prime's origins, namely that it started out as a regular Metroid on Tallon IV and was absorbed by the Phazon. I've cut out irrelevant (and spoilery) information, but the context here is that the "Leviathan" is the Phazon "seed" sent out from Phaaze, which impacted Tallon IV in the Impact Crater:

The Leviathan is capable of interstellar travel, creating wormholes in space to expedite the journey. Instinctively, it homes in on its planetary target. Shortly after impact, the bioform dies, leaving its armored shell to protect the Phazon core. Before it dies, the bioform often attracts and enthralls a large local predator. After mutating it through intense Phazon exposure, it compels the creature to protect the core. The core then begins to seep into the planet, replacing the local ecosystem with one based on Phazon.

  • Huh. I knew there was a plot hole there (played the US version) but never knew they attempted to correct it (and the splitting Metroids also showed adaptive abilities, so I never gave the armor any thought). Nice finds. – Radhil Apr 5 '17 at 11:52
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    Fantastic! I didn't realize i was quoting 2 versions. I had remembered it one way and had difficulty finding source material without actually turning on the game. – Premier Bromanov Apr 5 '17 at 14:25
  • @PremierBromanov Yeah, it's not so easy. You can compare these NA/NTSC logs with the corresponding PAL ones further down on the page, marked with "(New Lore)" – tobiasvl Apr 6 '17 at 13:41

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