They're three of science fiction's biggest — and most dissected — franchises. But have we been looking at them all wrong? A series of new fan theories suggests that there have been some strange underlying stories hiding in plain sight the whole time.

In response to this article, on the fan theories that were actually way better than the official versions, several commenters spun their own favorite alt-versions of how stories may have played out. Here are a few of our favorites.

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The Matrix

What was with all the plot holes in the Matrix sequels? Was it merely too many story threads running up against each other? A case of conflicting writers' visions? OR WAS THE CONSPIRACY JUST THAT MUCH BIGGER?

Interstellar

My favorite is the one where Neo actually hits his head leaving the telephone box at the end of The Matrix, and the two sequels are just a product of his unconscious, rabidly concussed, logic-compromised fever dreams.

(It's possible I just made this up.)

craigthejollyfatman

Everyone in the Matrix gets the Neo experience. The mind resists being trapped, so the illusion of freedom is given in unplugging and discovering "reality", the individual is given something to live for "Trinity" and something to fight for "Zion" giving the mind a sense of purpose. Death in the Matrix isn't a physical death but instead it is the mind finally ending its resistance and submitting fully to the matrix, giving up free will once and for all to become a part of a larger networked biological machine.

fiendishmuffin

I had my own theory right before the third movie came out. At the end of Matrix Reloaded, Neo takes down a sentinel in the real world with telekinetic powers. To me, that was B.S., UNLESS... they were all still in the Matrix – a second, backup world for those that escape the first. No one has actually woken up.

I thought the third movie would explore the idea that Neo would be the first person to actually wake up in the real world, where there are no killer machines, just people hooked up to computers. And the real kicker is that we were never subjugated by force, but did it to ourselves to escape how shitty we'd made the real world.

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Star Trek

Life aboard the Enterprise didn't wrap up the way we think it did — and it's maybe all the fault of Riker's reading habits, explained some commenters:

trent100

The last episode of Enterprise is not what historically happened to the First ship, it is rather a interactive holo-novel that Riker was using.

The last two Star Trek films are Holo-novels, 23 century fan fiction, created by Voyagers Doctor as light entertainment, for the crew on their way home.

Cthulhula

I always viewed Enterprise as not the history of Star Trek that lead into the Original series but the altered timeline that resulted from the events in First Contact. This is somewhat supported by the Borg from that movie showing up in the series. The temporal war is the result of all the various factions in the modern era (TNG) exploiting the ability of time travel. The paradoxes caused by all that time travel eventually built up on each other and when Spock travels back in time in the new movie series he shatters the fragile timeline which reforms in a way that makes some events occur like they should but the details are all jumbled up. Kirk dies saving the ship instead of Spock ect.

Brainlock

This would also explain how the "retro" tech of ENT is still yearsdecades ahead of TOS. Not to mention some obvious missteps like Kirk being born in space, not Iowa.

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Doctor Who

Whether you're a new, old, or both Doctor Who fan, this theory that hops all across space and time (and, yes, television shows) has something for all of us:

Patrick Farley

My favorite fan theory is the retcon of Peter Cushing's Doctor Who... The fellow we see in the movies was actually a Torchwood agent who scavenged together bits of alien technology to build his own TARDIS. He may or may not have suffered a memory fugue similar to that of Jackson Lake in "The Next Doctor" but in any case he assumed the identity of the mysterious Doctor, even to the point of erroneously naming himself with Torchwood's code name "Dr. Who."

Sharaz Jek

I've been operating under the assumption that the Peter Cushing Doctor is, in fact, the half-human Tennant Doctor. 10.5 and Rose work for Torchwood, and something goes wrong and Rose is killed. 10.5 goes mad with grief, and while he eventually recovers, most of his memories are gone. He retains scientific knowledge, however, and finds he has a drive — almost an obsession — with the idea of time travel. Time travel...and an almost magical blue box.

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