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SPOILERS AHOY!

Erol was brainwashed and used as a puppet by the Dark Makers
This would possibly explain his transition from how he was in 2 to suddenly wanting to destroy the world in 3, despite that in the second game while he did make all the wrong decisions he did want to protect the city and kill all the Metal Heads.

The war that the Aeropans were fighting was against the Metal Heads
Makes sense given that in-universe the Metal Heads are at war with Haven City- the Aeropans were also fighting that same war, and thus collaborated with Haven on the Dark Warrior Program. Only problem being, the program worked for Skyheed while it didn't for Haven, leading the Aeropans to become more militaristic and power hungry.

Crash Bandicoot, Jak, Uncharted and TLOU are all in the same universe
Crash takes place on a prehistoric Earth (explains the animals) and Jak takes place millions of years later when all most the Crash fauna gave gone extinct except for the plants which have become domesticated in Samos' hut.

Uncharted takes place in present day where some remnants of Crash and Jak (like wumpa fruit and precursor orbs) are present in the world but ridiculously rare.

TLOU takes place in an alternate timeline where Nate failed to stop the baddies in U1 from escaping with El Dorado with the spores/dust that makes people into runners. People then experimented on that to accidentally create the mutated Cordecepys Fungus in the game.

Meta-example - Ty the Tasmanian Tiger copied off of Jak and Daxter, or vice versa.
Either Ty the Tasmanian Tiger copied Jak and Daxter or vice versa. Think about it. Both of their first games had basically hub locations that branched out to different areas that you could only access after completing the last hub. Both of their second games were much more open world with quests strewn about the map. Finally, their third games were both very similar to their second games with the addition of a Darker and Edgier plotline and venturing out into some sort of wasteland.

Jak 3 is actually Jak's Dying Dream.
Everything you knew in Jak 3 and Beyond was all a hallucination. Damas and his men finding Jak's beacon was really a hallucination. In reality, the Metal heads killed off everyone in Haven. So in other words, the hero Ashlein knew really did die off in the Desert, forgotten, just like his friends.

Judging from the... strange way they treat each other, it's not that far off. All the dark eco they've come into contact with has physically and psychologically altered them. Who knows what kind of insanity it all may have caused, to the point where they... You get the idea.

The rift gate was a trap
It's generally accepted that the precursors fled the metal heads through the rift gate when they were defeated. But then why was the rift gate deactivated and locked behind a huge door when it was found? Also, the first thing Metal kor says when you open the gate at the start
"Finally the last rift gate has been opened"
The thing about time travel is that you don't have to wait for your exit to open, you can go to it at any time once you have an entrance. Also, when the rift rider went through, it made it's own vortex in the sky above Haven instead of coming out of a gate, so if you travel through you actually don't need an open exit at all. If the metal heads were waiting, they could not simply have been outside a gate looking for the right end.The precursors could have lured the metal heads through the gate, presumably by actually fleeing through it, if they had rift riders.Then they came back after the metal heads to carefully shut it behind them, trapping them in the rift since they did not have time travel themselves. They then locked the gate behind the door, and scattered the power cells needed to open it to make sure the metal heads couldn't accidentally be let loose, and then either left the planet completely, or retreated into the catacombs beneath.The rift rider Keira built presumably contained a device, possibly powered by the heart of Mar, which made the gate function as an exit, intended to be used once the precursors were ready to settle their score. The whole thing about hiding Jak in the past so he could stop the metal heads was Xanatos speed chess played over 300 years by the precursors, as the opening of the rift by Jak unleashed the metal heads on the future forcing them to send him back to before the metal heads were unleashed so he could grow up safely.

The precursors are actually near-powerless
There's obviously the bit that they depended on a 15 year old boy to save the world, but more relating to the joke when Tess is turned into an ottsel. The only power the precursors have shown is that of turning others into more precursors.
  • And trapping veger in a force field. Should also be noted that their technology seems powerful enough to make up.

The Dark Makers are robots.
Three versions to this WMG:
  • All the Dark Makers are robots.
  • Some of the Dark Makers are robots.
  • All the Dark Makers are some ambiguous biological-mechanical form of being.
Supporting Evidence:

1. The regular Dark Maker foes more closely resemble the Precursor Robot boss fought at the climax of Act One than they resemble the Precursors.

2. Cyber-Errol: "It seems that my digital self can communicate with these poor tortured minds quite well." Directly to the Dark Makers' minds, or through some more conventional communication link?

3. Strong physical resemblance and design themes between the Dark Maker's version of the Titan suit and the Dark Makers themselves.

4. The ambiguously biological-mechanical form of the Terraformers. They have the same number of eyes, general skin design and offensive capabilities. They're even referred to as Dark Makers by Cyber-Errol.

5. Admittedly, the regular Dark Maker mooks vanish when they are killed, just like the Metal Heads, the Freedom League guards and the Marauders. The flying ones, however, explode, much like the KG Robots, and the Terraformer blasts itself apart.

6. Terraformer has thrusters under its body, as well as detachable legs.

7. Can't claim this myself, as I haven't played TLF, but apparently Daxter's Dark Eco form looks nothing like a Dark Maker (will someone please confirm this?). If so, then since Dark Makers are corrupted Precursors, but Daxter is also one and yet looks nothing like the ones seen in Jak 3, presumably the real corrupted Dark Makers either were hidden or had sent the Dark Maker ship as a probe. Or TLF is Fan Discontinuity. You decide.

Verdict?

  • I've played TLF, and I can confirm that Dark Daxter looks nothing like the Dark Makers in Jak 3. But TLF is Fan Discontinuity in most circles as well, so I guess it doesn't matter.
    • Here's a picture of Dark Dax.
    • It is still possible that the actual duration of exposure matters. In TLF, Daxter spends mere minutes with his form being affected by the Dark Eco, while Dark Makers from Jak 3 would have been immersed in it for eons, certainly enough to change them beyond any recognition given the energy's unstable nature. And let's not forget that even a momentary exposure to the Dark Eco proved to be enough to transform Dax into an ottsel in the first place.

The events in Daxter are just Daxter spinning a yarn, and are highly exaggerated.
Implied in the last cutscene. Explains why there were no Metal Bugs or Kaeden in Jak 2 - Daxter did work as an exterminator, but he was just handling regular bugs with regular equipment to earn some cash, which he fluffed up into an epic tale of adventure about smiting mini-Metal Heads with flamethrowers and ultrasonic bug grenades in an effort to steal some limelight from badass "Metal Head Masher" Jak. Kaeden was a rival exterminator or other enemy of Daxter who got turned into a Big Bad for the sake of his story.

The in-universe reason for Keira's voice change.
Her vocal cords were damaged during the attack on Haven City in the prologue of Jak 3. Either from a stray eco bullet, the residue from the fall of the Palace or just being kicked in the throat. Fortunately, it wasn't too severe. But she was so embarrassed by the change that she decided to stay quiet for much of that time period. Thus explaining her decreased role in that games story.
  • Keira was officially 14 in The Precursor Legacy, and 18 by X. Her voice changed because she grew up.

The events in Daxter are just Daxter spinning a yarn, and are completely fictional.
Alternate version of the above WMG. Daxter really did spend those two years searching for Jak, and just made up a goofy, lighthearted story to tell Jak after the fact, either because he didn't want to trouble Jak with the real story of the horrible crap he went through as a tiny, nearly defenseless critter in a hostile, unfamiliar world, or because he's a braggart who can't resist telling outrageous tall tales. After all, the idea that Daxter really did forget about his best friend and spend almost two years goofing around while Jak was being tortured by Praxis? Ouch.

TLF takes place in an alternate universe that bears a coincidental resemblance to the J&D universe in some ways.
Hence the many differences in the world, character personalities.

Light eco powers in Jak 3 correspond to the powers given by all the other eco colors.
  • Green Eco = Healing
  • Blue Eco = Flash freeze (Jak isn't actually manipulating time, he's just cranking the blue eco speed boost up to eleven to get a Bullet Time effect. Notice how the screen gets tinted blue when flash freeze is used.)
  • Red Eco = Light shield (Red eco powers defensive weaponry in Jak X, including two shields that look nearly identical to Jak's light shield.)
  • Yellow Eco = The source of Jak's Very High Velocity Rounds when he shoots things while using flash freeze. Alternately, Jak might have the ability to shoot fireballs or something similar to the original yellow eco powers(he did it in the final battle of the first game, after all), but never had any need to discover/use it because the morph gun already serves that purpose.
Light flight is the only power exclusive to light eco.

The White Eco in TPL is what kept Jak alive and sane in Renegade
I believe that the White Eco is the only thing that kept Jak from mutating into an Eldritch Abomination in Jak II. We're never told directly what happened to the others (but oh God can we guess...), but Jak is different because of his exposure to a primordial, raw form of Light Eco. The White Eco stayed deep within his body, and when the Dark Eco started pulsing through him in measured quantities, the White Eco counteracted it.

Ottsel Dummy is Willard, the mentally challenged miner from TPL.

After Willard fell into a pool of dark eco and ended up as an ottsel, the Precursors took pity on him and allowed him to join their group, hence why Ottsel Dummy's intelligence level doesn't really match up with the Precursors' "godly beings" status.

Metal Head skull gems are actually Metal Head eggs.

The skull gems do resemble the Metal Head eggs Jak destroys at the strip mine, just smaller. The eggs at the strip mine might just be unnaturally bloated because of the large amounts of eco they were gorging on. The Metal Head life cycle goes like this: after breeding, the female carries around the fertilized egg until she dies, after which the egg pops off, absorbs the eco left behind by its parent's corpse, and eventually hatches into a new Metal Head. The only Metal Heads with skull gems were the "pregnant" ones, so to speak, hence why some of the Metal Heads dropped skull gems and some didn't. The Precursors wanted Jak to collect the skull gems and turn them over to their oracles so the eggs wouldn't get a chance to hatch.

The Skull gems are actually brains

  • Solid crystals being used in computers is a common trope, so why not as part of a metal monster's brain? all of the metal heads have exactly one gem in them, whether or not it actually drops on defeat. This even applies to the leader himself.

"Ottsel" is a word that Daxter made up himself, not the actual name for the precursor species.

I believe Daxter is the only one who actually says "ottsel" in any of the games, and that would explain both the "How does Daxter know what he was turned into if the precursors = ottsels thing is a big secret" and "Why can't a half-otter creature swim" Fridge Logic.

There are two types of ottsels: sentient "Precursor" ottsels and normal animal ottsels.

After all, if all ottsels were precursors, and the fact that the precursors are ottsels is a big secret, how would Daxter know what creature he had been turned into? Alternately, the Precursors could be the original ottsels, while the normal animal ottsels were other animals that were transformed into ottsels through eco exposure.

The precursors' goofiness(and maybe even their ottsel appearance) was an act put on to earn Jak's trust.

Jak was angry, bitter, recently traumatized and ridiculously powerful, not to mention quite experienced when it came to destroying precursor battle robots - in short, he was dangerous. Taking a cue from the one Jak was most devoted to, they imitated Daxter's antics to the best of their ability, hoping to endear themselves to Jak with the "small goofy orange creature" routine that he seemed to respond positively to and avoid Jak turning on them/relapsing into the "I'm through saving the world" mindset/otherwise screwing things up royally.

The light eco/Light Jak tamed Dark Jak.

Hence why his only use before Light Jak was mowing down legions of enemies, but after Light Jak the dark powers could be used to conveniently blast random obstacles out of the way or sneak around invisible.

Daxter's role is deeper than Plucky Comic Relief; his comforting familiarity/distracting goofiness/whathaveyou was the only thing keeping Jak sane from Jak 2 onward, particularly where Dark Jak was concerned.

Pretty common Fanon, and Daxter does seem to be the only one who gets many smiles(not of the "yay, I get to go kill something/blow something up/do something dangerous" variety) out of the rather angsty Jak, not mention snapping Jak right out of Dark Jak mode in the beginning of Jak 2, and safely riding on Dark Jak's shoulder while he goes berserk on hoards of enemies. Furthermore, it's possible that, as Jak became more comfortable with this new world he found himself in, had Dark Jak balanced out with Light Jak and began to form close bonds with people other than Daxter(particularly Keira), his need for Daxter diminished, hence the rather cold, dismissive behavior towards Daxter in TLF. (...or else HIG just doesn't know how to write Jak and Daxter's relationship.)

The Lost Frontier was somehow influenced by The Edge Chronicles.

Pointy-eared Sky Pirates on the edge of the world, eh? It could be a coincidence, but there's also precursor text on Phoenix's airship that translates to "open sky", a phrase repeated constantly throughout the Edge series.

Jak will eventually become his own ancestor via time travel, making the House of Mar a loop that begins and ends with Jak.

In other words, the answer to the "Is Jak Mar or a descendant of Mar?" question is "both."
  • We know Jak is descended, or at least related to Mar. He is referred to as the "Heir of Mar" in Jak II and Damas explicitly says in Jak 3 that he and, by extention, Jak, come from the House of Mar. So if Jak really is the original Mar, he is his own ancestor, no ifs or buts about it.
  • Plus he could just be named Mar after his original ancestor.
    • A compromise to how Jak/Mar can be his own ancestor without causing Fridge Squickiness could be via adoption of someone who will be his ancestor in the past as his son who then continues his legacy.note 
  • Other evidence for this theory includes:
    • Onin saying "Nice to see you again" when meeting Jak for the first time in Jak II
    • Samos hinting that Mar "may be closer than you think" at the end of Jak II
    • The Ottsel Dummy talking about Jak's future adventures, "or was it the past? *looks at camera*" at the end of Jak 3
    • At least one of the Precursor statues that give you side missions in Jak 3 says that "you were... I mean, are a great hero." upon mission completion

"Real" Precursor Orbs are actually small, coin-sized objects. They only appear large in-game to make them more convenient to collect, gameplay-wise.

Crazier things have been used as currency in real life, but paying for things with large quantities of football-sized artifacts still seems rather awkward.

Onin was once a Heroic Mime, like Jak originally was.

Furthermore, when Jak becomes old and sagely, he will become mute once more and become an Onin-like soothsayer, with Daxter his snarky interpreter.

Daxter is an orphan.

After all, we never saw his parents in TPL and they've never been mentioned. One would think that telling his parents would have been one of the first things they would have done after his transformation. Plus, he elected to stay in the future/present instead of going back to Sandover... wouldn't he at least have thought about seeing his family again before making that decision?

Jak's Uncle is Mar

It's very ambiguous whether Jak IS Mar or named after Mar. Personally, I like the latter the best since it gives off a more defined legacy, plus it gives Jak's Uncle a place in the actual timeline. Jak's Uncle could have been in cahoots with either Samos or the Precursors to watch over young Jak when he was sent to the future. Perhaps knowing of what's to come, he would create Haven City sometime after the 15-year-old Jak travels back to his true time period. True, there is a statue of Mar in Jak II who looks nothing like him, but I always chalked that up to people "fluffing up" the myth of Mar and creating what they assumed Mar looked like. I mean, it HAS been 300 years.
  • "I say, Jak old boy, if you happen to find any statues of your old uncle, be sure not to blow them up even if some fat man in a floaty chair tells you to, will you? Jolly good."

The Precursors can turn into beings of Light Eco, but choose to stay as Ottsels most of the time.

When Jak turns into his Light form he looks to be composed of pure Eco/Energy, kinda like the humanoid Precursor hologram we see at various points in the series. Daxter himself is proof that one with Precursor blood can transform into another form after being exposed to large amounts of eco, much like Jak and the people of Aeropa. It's possible that the Precursors are the Light Jak equivalent to the Dark Maker's Dark Jak, and that they just use the holograms because they don't feel like staying transformed all the time, preferring their Ottsel forms.
  • This would actually help explain why the Precursor Stone was considered by Kor, the mortal enemy of the Precursors, to be a Precursor Egg, and why it was able to generate so much energy. There really was a young Precursor in the Egg, it was just in its energy form, being used as a battery.

Jak losing a number of his Dark abilities at the start of Jak 3 is caused by heatstroke sustained in the Wasteland.

Such as Dark Giant and Invulnerability. After all, according to Damas he was very close to death.

The Jak and Daxter trilogy is set in the same universe as Star Control

The unnamed planet in the Jak and Daxter trilogy is littered with ancient ruins and artifacts left by a long gone ancient race referred to as the precursors. Though the precursor revelation in Jak 3 may cloud this.

The green sun in the sky is, in fact, the Green Sun
And the Precursors were the winners of a previous Sburb session, possibly one played by ottsels.

Kleiver was always a member of Mizo's gang.
He already fit the naming scheme, after all.

The Krimzon Guard were never aiming at Jak
Instead, they anticipated him moving out of the way of their fire, and aimed around him in hopes that he'd dodge right into their attacks.

Jak knew about Dark Dax all along
Remember when Jak and Dax first met Tym? The first thing Tym points out about Jak is that he's been tainted with dark eco. He could sense the eco inside of others. Maybe Jak can do the same. This would also explain why Jak stopped Daxter everytime he tried to bring his new powers up. If Daxter mentioned his powers in front of Skyheed they may have tried to experiment on Daxter. Sure, Jak didn't know that at the time, but what he did know was that Skyheed had an interest in him because of his powers. He protected Dax by keeping him out of Skyheed's interests. Then there was the time at the hangar when Jak found that kick ass jet. Jak was probably concerned about any surveillance that was in the hangar and anyone who might report Dax's condition to Skyheed. This also explains how Jak knows exactly where to be when Daxter changes back and tumbles out of the elevators he comes back out of at the end of the Dark Daxter sequences. When Dax finally changes in front of him Jak was unsuprised because he knew from the get go and only offered his support with that "Chew before you swallow" line because he knew what Daxter was going through.

The events of Jak 2 are a time-loop retcon as to how the kid was REALLY hidden in the past, which is that Samos and the Kid were from an alternate Bad Future where Haven was wiped out
NOTE: This theory contains a huge amount of potential Mind Screw and Fridge Horror due to the implications

Every stable time loop has to start somewhere, otherwise it would be a never-ending paradox. The first iteration of the loop was a Bad Future where Haven was completely destroyed by the Metal Heads, forcing a young Samos and Jak to escape via the Rift Gate, thus sparing themselves from being killed. Furthermore, there was no future Jak who would save Haven City because he didn't exist yet. Samos arrives in Sandover Village and starts all over by raising Jak (with both daxter and Keira being adopted from the village) so they can travel into the future and defeat Metal Kor, thus sending young Jak and Samos into the past to create a time loop. As a result, the original Bad Future which happened where everyone is killed by the Metal Heads is completely erased from continuity, with the events of Jak 2 being the Stable Time loop.

  • It might sound plausible that Metal Kor actually intended to have Jak's Rider enter the rift, assuming that he could've easily destroyed it with a single beam attack right there otherwise. Though it would also seem that Kor wasn't aware of two particular things when he approached Jak in the old man form: that Baron Praxis was plotting to double-cross him (a news delivered by Jak, which might otherwise be inconsequential if not for the Precursor Stone), and that the kid was actually Jak in his past (cue his surprise when the croca-dog responded affectionately to Jak while it wasn't taking nicely to anyone else but the kid). Which in turn implies that Kor might have extensive knowledge of previous time loops, whenever Jak ended up anywhere but around the kid, and each time the Precursor Stone remained outside his reach (since there was no one to pass the Tomb of Mar tests). Said time loops probably might've been counted by myriads, until by pure chance an opportunity to extract the Precursor Stone presented itself. Unfortunately for Kor, the Precursors themselves (and probably Onin through channeled visions) did also retain their knowledge of those very time loops, adjusting Jak's fate just so for him to have a chance to defeat the Hora-Quan leader once and for all (which he used well in the end).

Mar, the founder of Haven City, is mythical. Furthermore, the real Mar is not one identity, but rather a collection of individuals/groups that built Haven City and its parts.
  • This is comparable to the Yatagarasu of Ace Attorney: Investigations, where *spoiler alert* the thief is a collection of three individuals rather than one.
  • This stemmed from an idea of mine. I have always thought that Jak might not have been THE Mar, since he disappeared just as the rift gate was opened. I considered the individuals present in all the world's locations during Precursor Legacy (Uncle, Fisherman, Geologist, Warrior, Gambler, Blue, Red, and Yellow Sages,etc.), and developed the premise that they all would have needed to work together in order to establish a base of resistance against Metal Kor.
  • "Mar" need not be the inhabitants of Precursor Legacy's world per se. "Mar" might be either their descendants or the aforementioned inhabitants plus other individuals who were not encountered by Jak in the Precursor Legacy.
  • The "Mar" identity was created in order to justify centuries of traditionally strong, central authority for generations of future citizens. Haven City did not have an actual ruler before its completion, but one person was selected in order to be its first ruler. This may have been a man named Mar, whose family and lineage (House of Mar) ruled continuously until the reign of Damas and Praxis' betrayal, but one man was not responsible for the entire city's completion as asserted by most of Jak II and III's characters (i.e. Vin: "Mar built the shield walls and the eco-grid"). This idea was only created so that citizens would accept the concept of a ruler.
  • Alternatively, Mar could really be Jak and, the inhabitants, having known of his true identity from Samos (of course this knowledge would be hidden from Jak somehow), might name the mythical founder in his honor. This may be unlikely considering Samos' forethought; he is knowledgeable enough to know never to share such a secret.

Rainmaker and Blockade will adapt Jak and Daxter into a movie for 2017. Similar to how they are doing Ratchet & Clank for 2015 and Sly Cooper for 2016.

The Baron knew the Piercer Bomb would destroy the universe.
The Baron knew that the stone would destroy everything if cracked open. In fact he was counting on it. He knew that the metal-heads had overrun the world and it was just a matter of time until Haven City fell to them as well. By setting off a doomsday weapon, he was destroying the metal-heads as well, denying them their victory.
  • He could alternatively just fire some nukes at the nest. If he's too lazy to send out security tanks to the hideout.

Assuming it is not a reboot like Naughty Dog had originally proposed, the real Jak 4 will paint over The Lost Frontier with Broad Strokes and focus on the Sequel Hook of Jak X.
X has an unresolved yet extremely important plot twist and TFL was poorly received by the fanbase for a number of reasons. It's really a matter of common sense. You can still use choice elements from TLF like Keira being an up-and-coming eco sage and tie it into Rayn inheriting both Krew and Mizo's dirty businesses and running an even harsher crime empire in Kras City than her father did despite retaining an affinity for her old racing buddies (Jak most of all).

The Precursors built Treasure Planet.

It is revealed in Jak III that the planet is a giant mechanism with a powerful weapon at it's centre. The Precursors learned from their efforts building Treasure Planet and created a new world capable of sustaining itself. However, they didn't finish covering the mechanism with a layer of crust and mantle in some areas, creating the Brink in TLF.

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