From user wordofgreen:

1. George Lucas did an excellent job of hiding the truth of Vader being Luke’s father from people, down to filming the scene one way and then bringing a elect few back to do the scene again. So, if it is as you say and the idea was abandoned partway, it’s very plausible the number of people who knew the epic twist would be a scant few.
2. Given the size of Naboo and the fact the droids go only after the Naboo and not the Gungans, it is extremely unlikely Binks would just happen to be at the landing site of any federation ships, much less the ship carrying Qui Gon Gin. He can’t sense droids maybe, but I bet Master Qui Gon was a big bright beacon.
3. When Qui Gon sees him, those ships aren’t moving fast and all things around are fleeing. Jar Jar makes no attempt to flee, but instead waves his hands and blocks QG’s path, then clings to him. Afterward, he follows QG, pledges to be his servant and when told “that won’t be necessary” replies “oh, but it is, it’s demanded by the gods it is.”
4. His whole initial dialogue with the two jedi focuses on two points, A, that QG has saved him once, then again, and he owes him and must be his servant. B, the safest place is Gungan City, but Jar Jar will be in great danger and trouble if they go, setting himself up to go with them when they leave.
5. During the dialogue with Boss Nass, they cut to Jar Jar as Nass is talking, and Jar Jar gesticulates in his handcuffs, perhaps steering nass with the force.
6. QG “overdoes it” when he uses the force to calm Jar Jar when the third fish shows up. This conveniently gives Jar Jar an excuse to close his eyes and focus on taking control of the nearest bigger fish to come rescue all three of them. He wakes up and clears his head, dramatically shaking it off the very moment the fish 4 takes its first bite of fish 3 and the dnager to them has passed.
7. Honestly, I half suspected you’d somehow tweaked or altered the balcony scene as part of an elaborate hoax, but having just watched it twice Jar Jar is just as stealthy, then suddenly becomes a clutz in time to present a target and then jump away and land on the opposite side, complete with droid firing high then snapping its head to Jar Jar’s position.
8. On the way up the ramp to the ship during the escape scene, just prior to your hyperdrive sabotage theory moment, Jar Jar gestures, and then is the second person up the ramp following Amidala/her double, with her honor guard in tow. There is now way an un-jedi influenced personal queen’s guard is going to let a Gungan they just met, a race that hates Naboo, be between them and their queen, right?
9. The first thing Jar Jar says on Tattooine is, this sun is doing murder to meesa skin. He’s aquatic. Why the hell is he going with QG and R2 to the city to find parts? QG seems appalled at the idea of taking Padme, so why is he cool with taking the clumsy/bumbling Jar Jar? Perhaps because Jar Jar contrived to be there.
10. When Padme is at her most uncertain, it’s Jar Jar’s mention of the Gungan’s grand army that gives her the push to go back to Naboo, and coincidently make Jar Jar critical to her plan, as he is the only Gungan she knows.

From user CaliggyJack:

Star Wars is based off of films made by Akira Kurosawa. There is one thing very common in age old Japanese culture, dying for a purpose. Sometimes it is killing yourself, other times it is with assisted suicide, by willingly letting them kill you. In the OT Ben Kenobi lets Darth Vader kill him to spurn on Luke and motivate him through his continuing journey. The prequels were meant to rhyme with the OT.

Here’s the funny thing. As OP originally theorized, Yoda was the bumbling master of the OT and Jar Jar was meant to be that same idea for the prequels, but evil instead of good. Ben Kenobi commits honorable sacrifice to spurn on a youth in the first movie of the OT. Maul commits honorable sacrifice to spurn Obi-Wans hatred and determination to wipe out the Sith and carry on Qui-Gon’s legacy. Thus forcing him to train Anakin. Maul was only meant to kill Qui-Gon and then willingly die to Obi-Wan to kick start the events into Episode II.

Jar Jar may have used his ability to mind control on Darth Maul possibly on Tatooine, as that is the only time the two could have realistically met in that manner. Jar Jar didn’t need to worry about going out at night as the Jedi did not suspect him. There, Jar Jar plants in Maul’s head to die honorably at the hands of Obi-Wan after killing Qui-Gon. I don’t think Palpatine would waste a player in his game like Maul. All that effort for nothing? It seems more likely Jar Jar could have caused it. Perhaps he knew better than Palpatine on how the situation should play out? That is why Maul stands there silent without doing anything. When Obi-Wan begins to look at his lightsaber, Maul gazes at him in confusion. The basic answer would be because he had no idea why Kenobi wasn’t looking at him. However, any trained Jedi or Sith would no better than to forget the lightsaber next to him. Maul didn’t look confused because of that, he was confused because he was breaking Jar Jar’s mind control. By the time he actually broke it, it was too late.”

From user Aeromir:

This is my review of the prequels with the Darth Jar Jar theory in mind. For those of you who would rather read a synopsis than watch the whole movie, or to read along as you watch and see for yourself. I found a lot of things not mentioned in the original theory post. Notes inside “()”. More in comments.

Jar Jar is waiting for Qui Gon when he arrives, in the middle of the TF invasion and is placed perfectly in his path so that he cannot avoid him

Jar Jar says that he is Qui Gon’s servant, that he owes QG a life-debt, and follows them

JJ suggests that they go to Gungan City and leads the way

The Gungan Chief provides Qui Gon with a transport vessel, as Qui Gon and Obi Wan go to leave, JJ suggests to Qui Gon with a hand gesture that he will need a guide through the planets core. Obi Wan protests, yet Qui Gon insists that JJ is right, and speaks to the chief about JJ’s release. JJ confirms that he owes QG a life-debt, and the chief is forced to release him. (Jar Jar planned this all along, and just now mind tricked QG)

As they move towards the core, JJ explains that he was banished for being “clumsy”, using lots of hand gestures. They are attacked by a huge sea creature. Then another much larger sea beast attacks the original. (Could JJ be summoning these creatures to them with Mind Control?)

Qui Gon’s ship inexplicably loses power. JJ panics with lots of hand gestures. When the lights come back on, they are face to face with another sea monster. (Perhaps also summoned by JJ?) During the pursuit, JJ faints. Immediately after he faints, another, larger fish comes and attacks the fish pursuing them. (Could JJ be testing these Jedi by forcing them to respond to attacks and studying them? Possibly learning how they react and devising strategies to counter them)

Ambush scene (Why wouldn’t the Jedi leave him now that they have completed their journey through the core and JJ’s role as a guide has been completed?)

After entering the hangar, QG confronts the droids guarding the ships. He attempts a jedi mind trick and fails. As the battle starts we see JJ make a hand gesture. (Possibly a Force Push or Pull)

The crew steals a ship. OW tells JJ to stay in the droid bay.

As they head toward the blockade they’re attacked by blaster fire. The shield generators are damaged. The damage causes all of the droids to be activated and sent out of the droid bay to repair the damage. (Leaving JJ alone. Could JJ have manipulated the blaster fire to damage the shield generators, knowing that would activate the droid response and leave him unattended to disable the hyperdrive?)

Two droids are destroyed during the repair. A crewman comments that they’re “losing droids fast”. (More blaster manipulation by JJ, slowing down the repairs long enough for him to completely sabotage the hyperdrive) R2D2 fixes the shield generator.

Crewman reports that they don’t have enough fuel to get to Coruscant and that the hyperdrive is “leaking” (Sabotage by JJ). OW suggests Tattooine.

Padme is cleaning a damaged R2-D2. JJ enters and starts a conversation. (JJ must already know that she’s the actual queen charading as a double) When Padme asks him how he ended up here, JJ gives a rambling and nonsensical explanation with lots of hand gestures. (It’s possible that following this conversation, Padme is enthralled)

OW reports to QG that the hyperdrive is broken completely and will need to be replaced. (Holy shit this is why they end up going to Watto and meeting Anakin. JJ planned the whole thing.) Both jedi agree that they sense a disturbance in the force. (We’re led to believe that they’re sensing the arrival of Darth Maul, but this could be JJ as well)

As QG and JJ head into the city (why is JJ joining him?), the queen’s security officer follows them and says that the queen has requested that they take a handmaiden with them. QG protests, the officer insists, saying that the queen wishes to know more about the city. (The handmaiden in question is Padme, the actual queen. Perhaps she was Force manipulated into wanting to join them by JJ, ultimately setting up her introduction to Anakin). The security officer is uncomfortable, and we can tell he has a feeling that something strange is going on.

They enter Watto’s shop. JJ fumbles around with parts and droids. QG leaves to discuss a new hyperdrive with Watto, leaving JJ and Padme with Anakin. Padme and Anakin discuss his life of slavery. Padme angers Anakin by referring to him as a slave. Immediately after, JJ causes a scene by activating one of the droids and very dramatically and drunkenly falling over and into things. (This could have been a purposeful distraction from the conversation to prevent Anakin and Padme from getting off on the wrong foot, and protecting the future romance.)

As they go to leave the shop, JJ is fumbling around the shop to ridiculous levels, throwing things and falling for absolutely no reason. (Do droids make him uncomfortable maybe? Idk wtf is going on here. The situation doesn’t seem to call for JJ to distract from anything with crazy antics.)

They leave the shop. JJ attempts to eat one of the shop’s snacks without paying for it. The shopkeeper yells at him and, panicked, JJ launches the dead animal at Sebulba, who starts a fight with JJ. Anakin intervenes. QG and Anakin and introduced. (Totally engineered by JJ). A sandstorm is approaching and Anakin suggests that they find shelter at his home.

At Anakin’s home, he takes Padme and shows her his droid project, C3PO. She comments that the busted and incomplete droid is “perfect”. (Perhaps because she is enthralled by JJ and simply doing whatever she can to build the relationship with Anakin).

Anakin and crew are eating dinner. Anakin says that he is the only human who can podrace, and QG asserts that he must have jedi-like reflexes. Anakin guesses that QG is a jedi and says that he had a dream of becoming a jedi, then coming back home and freeing all the slaves. (So far as I know, JJ hasn’t been to Tattooine before this, so it’s unlikely that this dream was planted by him). They come up with a plan to make a bet with Watto on a podrace that will get them their hyperdrive.

Padme expresses disapproval at “trusting a boy we hardly know”. (Interesting that Padme toggles between this sort of disdain for Anakin and seemingly full-on infatuation. Could this be the difference between between her actively being mind controlled and having her own free will?)

Anakin’s friends comment that he’s been working on his podracer for years and it has never run.
JJ is seen carefully working on Anakin’s podracer. (WHAT THE ____?) As soon as Anakin warns him to be careful, JJ immediately reverts back to fumbling around and being clumsy, even getting his face caught in an electrical beam which numbs his tongue. He then gets his hand stuck in the engine. The droids comment that JJ is odd. Anakin attempts to start the podracer and succeeds. (Holy shit, this podracer has never started. JJ fixed the podracer so that Anakin could join the race.)

Darth Maul arrives on Tattooine. (Since JJ is working with Palpatine, it’s likely that he is aware of this. Look for any clues that might support this idea.)

Padme learns that Anakin has never even finished a podrace, and is extremely turned off to the idea to the idea of betting everything on him. QG reassures her. (Padme seems to be the voice of reason here. You’d think the jedi could find a better way to solve their situation that having to resort to all-or-nothing bets involving gangsters and endangering the lives of child slaves . Evidence for JJ pulling strings and directing the story).

Everyone prepares for the start of the podrace. We see JJ inexplicably working on the podracer again, unsupervised. Sebulba breaks something on Anakin’s podracer. (We assume that Sebulba’s sabotage is what causes Anakin’s podracer to malfunction at the start of the race, but even though the broken part is never actually repaired, the podracer comes back to life and performs better than every other podracer. Later on in the race, the part that Sebulba sabotaged -does- cause major damage. It’s possible that it was actually JJ’s sabotage that shut down the podracer at the start of the race, but I’m not sure what JJ’s goal would be in this case.)

After the race, QG tells Anakin and his mother that Anakin is free. When the mother asks if Anakin will become a Jedi, QG responds with “Yes. Our meeting was not a coincidence. Nothing happens by accident.”

Darth Maul ambushes QG and Anakin as they make their way back to the ship. We see everyone accounted for in the ship except for JJ. (Where JJ is during a Sith ambush could be important. That he is the only character missing and unaccounted for during this fight is big.)

Padme enters a room where JJ is asleep in a chair. She watches a message from Naboo saying that the death toll is catastrophic, begging them to respond. We then see Anakin sitting in the corner. He says that he’s very cold, prompting Padme to bring him a blanket. She says that he’s cold because he comes from a warm planet. This snowballs into a more intimate talk in which Padme tells Anakin about “the queen” being worried about her people. Anakin then gives her a gift, and they both relay that they care about the other. (Things seem to be moving awfully fast between these two, especially considering Anakin’s age. While it could make sense that Anakin is cold on the ship due to being attuned to warm weather, I think it’s more likely, especially considering JJ’s proximity in this scene, that JJ either used the Force to physically make Anakin cold, or more likely mind controlled Anakin into believing that he was cold. Force users in general show some resistance to mind control. Even without training, “The Chosen One” might be more difficult to control than a trained Jedi, but a master of mind control like JJ who is (we believe) capable of fully controlling massive sea creatures and enthralling trained Jedi Knights, should be able in a highly focused state (in this case, a feigned sleep), to manipulate young, untrained Anakin with ease.)

The crew arrives to meet Senator Palpatine. Jar Jar bows gracefully to him with the Jedi.

JJ and Anakin sit together just outside a meeting between queen Amidala and Senator Palpatine. (Why is JJ allowed to be here amongst these high-security politicians? They’re not even accompanying QG or OW at this point.) We see Anakin take JJ by the hand and walk off-screen, the two now seem to be good friends. Palpatine tells Amidala that the current state of the Senate is unlikely to offer her any aid on Naboo. Specifically, that the Supreme Chancellor is unable to act because of accusations of corruption marring his reputation. He suggests she issue a vote of no confidence and attempt to remove the Chancellor from office. Palpatine would then take his place and offer aid to the queen and Naboo. Amidala refuses.
QG and OW inform the council of the attack by Darth Maul. QG asserts that he believes his attacker was a Sith Lord. Two members of the council express disbelief, citing that the Sith have been gone for a millenia, and that they don’t believe the Sith could have resurfaced without their knowledge. Yoda ripostes with “Hard to see, the dark side is”.

Palpatine addresses the Senate alongside Amidala, attacking the Trade Federation and their invasion of Naboo. TF claims there is no proof and demands that the Senate send a commission to Naboo to ascertain the truth. The Supreme Chancellor talks in private as Palpatine tells Amidala that the Chancellor’s counselors are on the TF payroll. When the Chancellor agrees to the demands of the TF, Amidala is convinced that Palpatine is right and calls for a vote of no confidence in the Chancellor’s leadership to remove him from office.

We see QG and OW discussing Anakin. OW advises QG not to defy the council, “not again”. (It’s implied here that QG has a history of defying the council. No details are given, but perhaps it was this trait that made QG a target for JJ to enthrall. Someone who could make the suggestion to train Anakin to the council, but wouldn’t be out of character or suspicious, and thus less of a risk to JJ’s plans.)

JJ and Amidala discuss the war on Naboo. JJ reminds her of the Gungan’s “Grand Army”. Palpatine then enters and explains that he has been nominated to become the Supreme Chancellor. They then begin to discuss political moves and she says that she is going back to Naboo. (JJ is present in the background during this conversation. Why is he always allowed to be a part of what should be and does seem to be considered sensitive information? JJ is one of 5 people in the room for this conversation.)

In the Jedi Council chamber, QG, OW, and Anakin are told that Anakin will not be trained as a Jedi because he is too old. QG protests saying “He is the chosen one. You must see it”. Yoda responds that the boy’s future is clouded. QG says that he will take Anakin as his padawan. When Mace reminds QG that the Jedi Code forbids having two apprentices, QG says that OW is ready to become a Jedi Knight and that there is little more OW can learn from him. (We see this as QG fully believing in and supporting Anakin, but that the council and even OW aren’t convinced might give us some information. This is the result of JJ’s enthrallment of QG. He is entirely convinced that Anakin isn’t a danger, though the truth might (MIGHT) be closer to what everyone else (who aren’t actively being mind controlled) perceives. Anyone else might be considered crazy and the council would be alerted to Sith mind control, but QG is just being defiant to the council again. Seeing how QG behaves towards the council also teaches Anakin not to take their word as law, and begins to sow the seeds of distrust in the Jedi Order from the very beginning.)

QG and OW exit a ship as OW again expresses concern that “It’s not disrespect, Master, it’s the truth… the boy is dangerous. They all sense it, why can’t you?”. QG responds “His future is uncertain. He’s not dangerous.” (Even OW can see that something is up with QG)

Amidala, OW, QG and JJ head back to Naboo. Everyone is concerned with Amidala’s decision to return, explaining that she’ll be arrested and forced to sign the treaty the moment they land. The queen’s response is “We’ll take back what is ours”. (This makes no sense. The queen must definitely be enthralled as well. This is further evidenced by…) The queen then calls on JJ and says that she needs his help.

From user twothumbs:

• Darth Maul didn’t spy, he tailed the group in Tatooine, but he wasn’t creeping in the shadows, looking and listening from a vantage point. He makes no effort to attempt any of these things except a couple of incidences to be mentioned later.
• Jar Jar has been in the party and attaches himself to qua gon. No obi or Yoda or anyone else. His main focus is qua gon. Why?
• Qui-Gonn working on secret immortality technique which is instrumental and vital to the entire series, WHILE Jar jar is with him and finishes his research, again while Jar Jar is with him.
• Jar Jar is set up perfectly not only an influence but a spy. BUT if he is spying how does he relay orders to maul with out arousing suspicion?
• Before attacking the Jedi, Maul does 2 things. First he looks through his binoculars and watches the ship, but he’s not looking for either Jedi. Through the binoculars he sees Jar Jar, Padme and Ani. If he’s there for the Jedi then don’t you think the one time he’s looking through those binoculars he’d be looking for the Jedi at not Jar Jar? Maul isn’t an amateur. HE didn’t make a mistake. He’s looking for Jar Jar, because Jar Jar is the man on the inside, he’s looking to make contact with Jar Jar. How do we know?
• After looking through the binoculars, Maul later sends a drone. I ask you, what can that drone do that the binoculars couldnt? The drone can make contact, deliver instructions, promise rewards, which Maul dare not question.