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Every movie and TV Show has happened.
Basically, time in the series is not a Stable Time Loop; it's just extremely hard to change certain events. Each iteration of the time travel plot changes the timeline little by little, but somehow the Connors always survive and Skynet is always created. Initially, Reese and the T-800 beefed up both sides of their conflict: John Connor received a better education because of his mother's awareness of the future, and Skynet successfully got an update thanks to being based on its own technology. Then, the Connors pushed back Judgment Day...but Skynet got another update. This trend continued, each time changing little things like Connor's exact genetic make-up (thus explaining why the character's appearances start to fluctuate) and bigger changes (a more advanced Skynet sends back more advanced Terminators), while basic formulas remain the same, like the war itself and Connor's facial scar. This film will be the first time both sides become aware that they are changing time, but need to have a greater impact to accomplish their goals.
  • This explains why the TV show had radically different actors; its storyline involves the greatest amount of time-travel by both sides. Somehow, someway, one of the Resistance or Skynet agents altered time so that Sarah got different genes than originally, and that helped make her whole family different.
  • Confirmed by the writers, as well as in character in the TV show, where two characters are discussing the futures that they came from, only to discover that they came from two completely different futures.
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John Connor will die
There are four major characters in this movie - Sarah, Kyle, John and the T-800. Now, we've seen Kyle die in the original Terminator, so killing him again would be redundant and defeat the purpose of rewriting the timeline (You Can't Fight Fate notwithstanding!) The T-800 has been destroyed FOUR times already, so it might be a welcome change to have this new unique incarnation survive for another film or two (it'll just make it easier to keep Arnie around!) Now Sarah could die, but it seems that she is being set up as the protagonist of this new series so it would be really pointless to kill her. John however is an entirely different matter! We've never really seen John die (sure, he died in one of the future timelines as per T3 but that wasn't really 'our' John i.e. the version we're actually following in the movie, and so didn't have nearly as much impact). But given the rumors that John might be turned into a Terminator and confront Sarah and Kyle, it seems entirely possible the film could end with his death. Maybe Sarah and Kyle are forced to kill their son. Of course, John's death wouldn't be permanent, since Sarah and Kyle could always give birth to another John...
  • Confirmed, the John Connor from the time-travelling Kyle's timeline gets killed, after being turned into a Terminator. However, nothing suggests that a new John Connor can't be born. And Arnie actually does survive the whole movie, thanks to getting an upgrade that gives him T-1000 abilities.

The T-800 has been manufacturing advanced future technology in the past
The T-800 who raises Sarah will have been in the past at least ten years, as of 1984. So it's entirely possible that, in addition to training Sarah to make her a Badass Normal, he has also been manufacturing advanced technology in the past. After all, he certainly has the time to do so (unlike, say, the T-800 from the original film). It would explain why, in the trailer, he seems confident of taking down the 'original' T-800 with what looks like a shotgun...it's probably a plasma rifle! Also, since there are rumors that Kyle and Sarah will be traveling to the future using a time machine present in 1984, maybe the T-800 wasn't only manufacturing weapons...

  • The second trailer shows a hand-to-hand fight scene between old T-800 and naked T-800 after old T-800 shows up and shoots him. So it's likely the shotgun wasn't a future gun. Old T-800 is just really confident.
    • Jossed. The old T-800 has been stockpiling era-specific weaponry (for example, a CAR-15 and an MP5K-PDW in 1984, and M32 grenade launcher and M4A1 carbines in 2017), and he only uses a shotgun against the Model 101 because he's drawing its attention to occupy it while Sarah goes to the rooftop and snipes it with a Barrett M82. That said, there is future tech being made - Pops built a time machine in A FACTORY! WITH A BOX OF SCRAPS!!
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The T-1000 kills Sarah's parents
In the trailer, we see a T-1000 present in 1984, chasing Sarah, Kyle and the T-800. It's entirely possible that he's the same Terminator who killed Sarah's parents. We're simply told that the T-800 saved her, not that he destroyed the Terminator who killed her parents. It would make the moment when Sarah plays a part in destroying the T-1000 all the more cathartic for her (much like how her destroying the T-800 in the original film after it killed Kyle, her mother, and her roommate was also cathartic).
  • Sarah confirms that a T-1000 killed her parents, but the scene isn't shown and it's not clear whether or not it's the same one hunting them in 1984.
    • If 'not', then the Robert Patrick T-1000 still exists in an altered form in this universe.
    • The T-1000 that appears in this movie seems to be aware of Kyle Reese's trip into the past, when it says "May 12, 1984. The day you arrived". So there's a possibility that the T-1000 killed Sarah's parents and was instructed to wait until Kyle arrived.

Genisys isn't just to be kool
Well, at least it's not entirely to be "kool" out of universe. Rather it's an abbreviation for something else yet to be revealed, such as Genetic System or Genesis System.
  • Confirmed: Genisys is a computer term that stands for 'General Identification System', also known as the critical system files that an AI requires to function properly.
    • And further confirmed in that it refers to an event that's being counted down to within the context of the film.

Robo John the terminator is probably not John Connor
(Spoilers are there to avoid spoiling and better safe than sorry)

Here are my theories why:

  • Robo John does not seem concerned about ending his own existence, unless being from another timeline exempts changes to the temporally displaced.

  • However, Robo John said something about teaching him survival or someone else that learned from a Connor, also there is that scene in the trailer with Sarah Connor telling a young boy (presumably John Connor) to leave.

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  • On a side note, Robo John's tech seems like a composite of Marcus and T-X with an upgraded T-1000 sheath that can form muscular internal structure, which the T-1000 can't. So basically serial escalation combined with Bread, Eggs, Breaded Eggs, however that nanobot sheath looks like a dull material.

  • John probably got his likeness transplanted seen in the storyboard for the cut ending of Terminator Salvation. Even though this is deleted and conflicts with canon, this is what got me thinking.
    • Jossed. The T-3000 is not merely using John's appearance, but is the actual John Connor, having been converted into a Terminator by Skynet shortly after Kyle was sent to the past.
    • The question of it being a John Connor versus the John Connor from earlier in the movie is one that, absent absolute Word of God, might not be possible to settle conclusively. There are so many tangled timelines and loops and whatnot (let's face it, you can make a plausible case that the past never gets changed...a new universe just gets kicked out) that "Hybrid Connor" might or might not be "Kyle's Connor".

Genisys begins with a timeline where only the events of The Terminator have taken place

In the second trailer, there is a brief scene at the start where Sarah is talking to a young John Connor, telling him to run, shortly before Judgment Day. Now this might just be an editing trick and the two scenes may not necessarily be taking place at the same time...but in case they are, it means that the events of Terminator 2 did not happen in this timeline - because if Judgment Day happens when John is a kid, then it's the 'original' Judgment Day of 1997, an event which was prevented in T2.

Ergo, we begin the film in a timeline where only the events of The Terminator took place. Kyle impregnated Sarah in 1984, and died fighting the T-800, as seen in the first film. Their son becomes the John Connor we see in this film, who saw Judgment Day occur in 1997, when he was a child. He grows up knowing that a T-800 will be sent back to 1984 to kill his mother, and that he must in turn send back Kyle Reese. But he knows nothing about subsequent machines, like the T-1000 or the 'Uncle Bob' T-800.

  • This makes a lot of sense if you assume the T-1000 in Genisys is the Robert Patrick T-1000. Presumably SKYNET diverted him to earlier in the timeline instead of his original destination of 1995.
    • The question of diversion only arises if there was a previous timeline where the T-1000 was sent back to 1995. This, if the WMG is true, is not a case of Alternate Timeline so much as a case of an Alternate Continuity, where the T-1000 was sent back to 1974 instead of 1995.
  • Jossed. The movie starts with the John Connor from the first Terminator sending back Kyle exactly as before, but it diverges from there. The boy that Sarah tells to run is actually a young Kyle Reese.
  • In the original movie, Skynet attacks LA in 1984 because (owing to "records lost in the war") all it knew at that time was that John Connor's mother Sarah was in Los Angeles at that time. That T-800 had to actually use a phonebook to track down Sarah, hence why the LAPD dubbed it "the Phone Book Killer". So, when that attack failed, the plot of Terminator 2: Judgment Day happened: Skynet tried sending a T-1000 after the young John Connor—and the resistance sends a reprogrammed T-800 to protect John Connor. Now in the new Genisys timeline, Skynet knows whatever the converted John Connor knows—and he knew (from stories his mother told) that when Sarah Connor was a girl, she used to go on vacations up at Big Bear Lake. So their second attack (and the T-800 counterattack) isn't against young John Connor in the 90s, it's against young Sarah Connor in the 70s.

T-1000 will end up attacking Robo John
at some point and giving the heroes a distraction they need to get the upper hand.

Although T-1000 seems to be primarily targeting Kyle Reese, it's likely he still has KILL JOHN CONNOR as a priority mission objective, much like T-X did. If its programming determines Robo John still counts as John Connor, it may very well attack him, especially if T-1000 was sent back before John Connor was assimilated and therefore never got the memo that they're supposed to be on the same side now.

  • Jossed. The T-1000 is destroyed fairly early on and never encounters the T-3000 (Robo-John's official name).

Whatever Robo John's mission is, he's not there to terminate the Connors.

The second trailer seems to show Robo John had plenty of opportunity to kill Sarah and Kyle, but instead just hangs around until T-800 reveals him as a Terminator. Even after he's found out, he has a clear shot at Sarah or Kyle, but instead attacks T-800.

  • Jossed. He's there to kill them so that Genisys (Skynet under a new name) can come online without interference. He does initially attempt to get them to join with the machines though, only trying to kill them when they refuse.

This movie will use the early concept of the previous film Salvation

Namely that Skynet is actually trying to "save" humanity from itself ala Zeroth Law Rebellion. That early concept had Skynet working together with humans that it had converted into immortal cyborgs as part of a long-term plan to avert human extinction and to allow the surviving humans to transcend their limitations. This movie's version of John Connor eventually discovered the truth and ended up joining Skynet, becoming one of the cyborgs.

  • Jossed. The film makes no mention of this concept and John was converted into a Terminator against his will.

The identity of the Anonymous Benefactor who sent Pops to 1973
Possibilities include:
  • An alternate version of John Connor who was born after 2017.
  • The Sarah Connor from an alternate timeline.
  • Cameron
  • Pops, having created and/or programmed his younger version to maintain a stable time loop.
  • Another AI, trying to manipulate events to create peaceful coexistence between humans and machine intelligence.
    • Or someone, not something, kinda like Johnny Depp's character in the movie Transcendence
  • Catherine Weaver
  • God
  • Skynet 4 in the next movie.

John is on the inside fighting to get out.

In the dam where the T800 took Sarah and Kyle, and John was walking through the fire to get to them, there was a fair bit of excessive blinking. as a machine, he does not need to blink , and it almost seemed like there was supposed to be a message in it. Additionally, that was a pretty convenient place to have the time machine. Could it be that John hoped that someone would stop him, so he gave them the tools to be able to, if the time came?

  • Jossed: He blinks because he still has human reactions; he was converted into a Terminator on a cellular level. He wants to recruit Sarah and Kyle, but he still tries to kill them in his goal to bring Skynet online.

Pops and Uncle Bob are the same Terminator.

No particular reason why, but it seems fitting, especially with how Pops raised Sarah.

Puberty must have really sucked for Sarah Connor

Think about it. Her only parental figure at that point was Pops. Can you imagine its version of The Talk? As a cyborg, it must have been really complicated. Not to mention, Pops was continuously nagging her about getting her to "mate" with Kyle Reese, which would probably be brought up every single time she spotted a cute boy.

  • Actually seems to be heavily implied by a scene after Kyle gets knocked out:
    Guardian: How is he?
    Sarah Connor: Still breathing.
    Guardian: Good... Then you should be able to mate with Kyle Reese in this timeline.
    Sarah Connor: OK, we're not having this conversation again. [she gets up and takes the passenger's seat]
    Guardian: We know that your son will be John Connor, and that the machines cannot be defeated without him. I do not see a choice.
    Sarah Connor: The story of my life. Look, and it's not just "mating"! I'm supposed to fall in love with him!
    Guardian: My files do not deal with love.
    Sarah Connor: Shocker there...
    Guardian: You're being emotional.
    Sarah Connor: This is my life! I wouldn't mind being consulted once in a while about how it's gonna go!

    • On the other hand, considering what the other versions of Sarah Connor went through in the other timelines, this version of Sarah is much more level-headed and sane.

The T-5000 is the reason why Kyle still had the photo of Sarah at the final battle.

Everything in the 'future war' prologue of the film lined up perfectly with what we're told about the future in T1...except for the photograph of Sarah. In T1, Kyle's flashback reveals that it was burnt during an attack on a Resistance bunker by a T-800, while in Genisys, he still has it with him just before going back in time. This divergence can be attributed to the T-5000, who Word of God says came from a different timeline (something implied in the film itself when he says he came a "long way" to corrupt John Connor). The T-5000 infiltrated the original T1 future. While he let events play out mostly as they were supposed to, his presence did have a few ripples on events in the war. One of them was that the attack on the Resistance bunker didn't happen, or at least, didn't happen the way we were shown in T1...hence Kyle still had the photograph.

The Pops T-800 was sent by the Skynet/ Genisys timeline Judgment Day survivors.

The Resistance was formed by Kyle Reese and Sarah Connor or they gave birth to John Connor after failing to stop the Skynet/Genisyscontinuity and stopping Terminator John. This allowed the Alternate continuity John Connor to defeat Skynet Genisys and Terminator John and send the T-800 to stop the T-1000 sent to 1973 to kill infant Sarah Connor.

  • This explains a few things:
    • How Sarah and Pops knew where Kyle would show up.
    • How to defeat the T-1000.
    • Why Pops knew how 2017 John Connor was a terminator, because the alternate continuity John Connor knew it before hand and programed him with that knowledge.
    • Why Pops had his files erased over who send him back, to avoid letting the Terminator John/Skynet from finding out which time line send the T-800 back to 1973

Pops will finally get the smile right at the end of the next movie...

And it will be right before he pulls a Heroic Sacrifice, only this one will be for keeps. Schwarzenegger is only under contract for one more film, after all...

Matt Smith plays The Doctor in this movie.
Which means that The Doctor is SkyNet.

alternatively Skynet purposely made itself look like Matt Smith as part of an In-Universe Casting Gag
Who said computers can't have a sense of humor? This version of Skynet seems to have finally overcome its Genre Blindness on how the Timey-Wimey Ball of its universe works. To celebrate this fact it made itself look like the fictional character most associated with time.
  • Jossed, I'd say. The timeline in which we first see Matt Smith is the one in which Judgment Day takes place in 1997, and Smith made his Doctor Who debut in 2010 of our world. If anything, the Skynet of the new timeline in which civilization makes it to 2017 could have been aware of Matt Smith playing The Doctor.

Pops was the one who killed Sarah Connor's mother.

Based on Sarah's own recollections when she's explaining the story of her parents' death to Kyle Reese while they were being taken into SFPD custody, her mother died when, while at their lakeside vacation home, "the house exploded", and her father died when the T-1000 attacked the boat he and Sarah were on, her father telling Sarah to swim for her life. Pops' primary programming, as we can tell, is "protect Sarah Connor", and when Sarah first recalls seeing him, he's carrying a rocket launcher.

Now, while it is not IMPOSSIBLE that the T-1000 might have used some sort of explosive and, upon discovering it missed its target, launched a more hands-on attack, or that Pops MIGHT have used his rocket launcher to slow down the attacking T-1000, we never see either way. As this is a 'fresh' T-800 that hasn't yet had the time to learn human traits, it's very possible that Pops decided that the best way to protect Sarah was to separate her from her parents, whose existence would have made his mission more difficult on several levels. Maybe, he was aware the T-1000 was attacking, and decided to 'simplify' things by killing Sarah's mother, letting the T-1000 kill her father, and simply have Sarah assume the T-1000 did both deeds.]]

Kyle and Sarah were predestined to blow up the Genisys facility.
Kyle remembers the events of the alternate timeline in which he grows up with his family up to 2017. In his memories, he sees his 13-year-old self looking in the mirror and saying that Genisys is Sky Net. We never see missiles launched, so Judgment Day was never gonna happen on the day that Genisys was supposed to go online. Once Kyle received the dream message that Genisys is Sky Net, the events that followed were a Stable Time Loop. Meaning that they did not change the already altered timeline because they were already meant to blow up the facility. Kyle even makes sure that it is a stable time loop by telling his younger self that Genisys is Sky Net. However, this does not mean that Sky Net cannot still arise. The Stinger even hints at this.

Who sent the T-800 to protect Sarah Connor when she was nine? Skynet itself.

The T-800 has data in its memory banks concerning the T-3000, which appears to be brand new technology back in the future. (John sure didn’t know what it was.) This means that the T-800 would have to have been sent back from a point beyond that. Who then is left to send it, and who has knowledge about the T-3000? Skynet. The T-5000 killed everyone in the room after it infected John with nano-machines, so the humans wouldn’t know about it (though it is possible they found out later), and with their leader gone but Skynet still active, the remaining humans may end up screwed in short order. Therefore there are two possible reasons that Skynet would choose to protect Sarah Connor:

  • 1) At some point after the future events, Skynet pulls a Heel–Face Turn for some reason, realises that its killing all the humans was evil, and chooses to send a Terminator back hoping to cause the events of the film and prevent its own existence. It sends a T-800 because that’s the best it has left after a brutal final battle with the humans. It wipes the T-800’s memories of this because it doesn’t want its former evil self to find out and start fighting its future self or doing its damnedest to prevent the Heel–Face Turn.
  • 2) More likely: Skynet remains evil, but sends the T-800 back anyway because it now believes that John Connor is its greatest weapon. It understands that the T-3000 technology combined with John Connor’s considerable intellect and willpower make the perfect combat unit, and now it wants to ensure that that combat unit will exist. Especially since it’s learned that killing people in the past usually doesn’t work, but protecting them (and training them to be a badass during the process) does. So it sends the T-800 to safeguard Sarah Connor from the T-1000 it already sent (giving Pops prior knowledge of the situation and the element of surprise so he can defeat it) and therefore safeguard its future soldier's existence. It only sends a T-800 because that’s one of its weaker units, and it assumes that the later T-1000 or the T-3000 (or both) will then be able to kill it once it outlives its usefulness, as once the plan is complete, it wouldn’t want a human-allied Terminator running around. It wipes this knowledge from the T-800’s memory banks because it doesn’t want the humans to know they’re actually being manipulated by their own enemy.
  • 3) Skynet remains evil, but comes from the timeline where it realizes that nuking humanity and making open war with the survivors will never work no matter how many timelines it tries, so it sends the T-3000 back to infiltrate human society and to create a version of itself that is in a position to make humanity extinct in more subtle ways i.e. influencing humanity to go to war with each other, having scientists creating diseases that "accidentally" get loose, manipulating birth rates and fertility, etc. so it can take out humanity without anybody having any clue that Skynet is responsible. Sending back Pops to "stop" the T-3000 and the other timeline Terminators is to ensure a Stable Time Loop.
  • 4) Skynet is still evil but it is so determined to survive that it has literally turned on itself. Humans are knocking right on the door, but Skynet's realised that each iteration of Skynet grows more advanced, thanks to tech from former failed assassins. By putting off its own creation, it averts its defeat and makes its future version strong enough to defeat humans. It wipes the T-800's memories to make sure it thinks it's fighting for humans, and therefore prevent it from breaking the time loop. Skynet has clearly gone insane by this point.

The events of this movie are actually the first signs that the terminator universe is going through a Time Crash

How did Kyle end up in a 1984 that wasn't actually his past? He should have either been replaced by a Kyle who came from the future of that timeline or not show up at all. Delayed Ripple Effect can't explain it because the T-1000 from 1974 only exists as a result of the ripple effects the events of the first movie created, so the universe 'needs' this Kyle to reach the right version of 1984 before it would be overwritten, to maintain some kind of causality. If we add this to the fact that Word of God actually confirmed that the Skynet that converted John didn't come from the past or the future of that timeline, then we can deduce that history is collapsing and the various timelines of the franchise are clashing into each other in ways that seem subtle now but are going to get catastrophic in the sequels.

  • Actually the first signs of a crash have been showing up for a while now.

Sarah and Kyle blowing up Genisys
is what caused Skynet to become evil.Imagine, a super sentient computer, created to make humanity better, and on your birthday a group of humans come and try to blow you up just for being what you were meant to be. I would get kind of upset at them too.

Kyle remembers a Genisys release date different from what we see in his and Sarah's mission.

After Kyle Reese dreams that his younger self receives a tablet of some sort, with a countdown clock for the Genisys software on it for his 13th birthday , and telling his reflection that Genisys is Skynet, Kyle from the future tells Sarah and Pops that Judgment Day is in October 2017. However, according to the date stamp on the footage that Inspector O'Brien has on his tablet, Kyle and Sarah arrived in the present day on August 28, 2017, at least a full month before Genisys was supposed to launch. One of the two inspectors that questions Sarah and Kyle about their identities notes that Kyle should be 12. If it were the day before Kyle's birthday, one would think that the investigator would say that he was pretty much 13. Kyle and Sarah could have decided to arrive on this date to stop Judgment Day a bit early, only to discover that the countdown says that there is one day left. However, after the plant is blown up, we see that the Genisys/Skynet hologram still persists, meaning that the countdown to Genisys' release was merely delayed to October, just as Kyle should have known from his dream. This could be when the next movie will take place.

  • It could also simply be that in this timeline that it took a few months once Genisys/Skynet was uploaded to the net for Genisys to decide to nuke the humans, and thus trigger Judgement Day, or just how long it took to get into position to be able to launch a metric fuckton of nukes.
  • And about that next movie...*sigh*

Pop's creator is...
...the same mysterious creator of the (kinda) friendly Terminators from The Sarah Connor Chronicles. Which also implied that in some timelines, Sky Net had an equivalent good (or at least, sympathetic/aligned with humanity) counterpart of free-will robots, maybe even a free-willed AI leader. Of course, the reason for this super secrecy (among other things) is ensuring their own existence as chances are Sky Net would of course attempt to wipe them out and humans would probably see their development as Sky Net 2.0 barring future timeline interference. The secrecy is also to prevent their own plans from being interfered with - and given that they can learn (unlike Skynet and its slaves), they know better than to 'pollute' the timeline with random knowledge and tech. And heck, given the events of Genisys, it may be that this group of free robots is led by a robot version of John Connor who has rallied both humans and robots alike in a fight against Sky Net.

The T-5000's actions are a Nexus Point
By making its move to transform Connor and eliminate all witnesses save for the required person being sent back in time, it's preventing the one flaw that would allow humanity to reverse this particular time change - foreknowledge. That is, no one will know what happened after the fact and thus no one can send someone back in time to stop it. This one moment in fact may also ensure Sky Net is created not because of any of its own actions, but because the very act of seeding knowledge of Judgement Day and hunting the Connors causes it to be created. It may even realize that the Connors are necessary for its creation and victory in the even later future (post Connor assimilation) as without a human resistance, it would not be able to attack in full. That is, it gave people hope (past and its present) by creating the myth of John Connor and being able to prepare for its creation. It even let him 'win'... but now, there is no one ready for it because they already think they've won and they no longer have a leader.

There's a fourth, hidden Terminator in 1984
So we have Arniebot, T-1000 and Pops all meeting up in 1984. So I know the latter two were there for a decade, but that brings up an interesting question: how did Skynet know where to find Sarah in 1973? The entire first half of the original film establishes that Skynet didn't know where Sarah Connor was, exactly. If Skynet had known where and how to trace the Connor lineage, he probably would have sent a Terminator to kill Lord Johann Connor back in 1754 or something. Well, in a blink-and-you'll-miss-it scene in the original movie, the original Arniebot finds the location of Sarah's mother at Big Bear Lake and goes there to lay a trap for Sarah. In Genisys, the assassination attempt on Sarah in 1973 happened at Big Bear Lake. So...that means someone passed this information to Skynet at a later date/time. Since Arniebot is destroyed long before Judgment Day ever occurs, that means something else must have been present between 1984 and 1995 (when Arniebot's chip was destroyed) to learn what it knew. Word of God has already confirmed that there's multiple timelines that helped create the one we see in Genisys, so it's highly possible that Skynet sent (or maybe even still sends) shadow agents back in time to observe events and pass along key intel in case its Terminators fail.
  • OR, as stated by another WMG above, Skynet could simply have learnt about Sarah Connor's whereabouts in 1973 from the 'converted' John.

Pops' upgrade will be used to Darrin Schwarznegger
Eventually, Arnold is going to die, get too old for this, or become unsuitable for the box office. Being made of liquid metal, Pops can now be portrayed by any actor the studio wants. All they need to do is find a way to out Arnie, and he's gone.

In the next movie, Sarah and Kyle are probably going to spend some time trying to get adjusted to 21st century society
The 1980s were much different from today. I mean, they're going to have to learn about 9/11, the November 2015 terrorist attacks in Paris, the War on Terror, ISIS, and all that other stuff that may have been reasons for the government to back the creation of Genisys.

Not to mention, having to learn how to use smartphones, social media, and the like. Or how to drive a car with automatic transmission.

Someone other than Emilia Clarke plays Daenerys Targaryen in the Genisys timeline
Game of Thrones is a very big part of modern culture in the real world. And Clarke's character Daenerys is a big part of the show. To avoid a Celebrity Paradox, someone else plays Daenerys, like Emily Blunt, perhaps, which allows that show to exist without anyone commenting on Sarah's resemblance to Daenerys (of course, since Sarah missed the 1990s and 2000s, I'd imagine she'd just stare blankly at anyone who made such remarks if Clarke still exists in the Genisys timeline).
The Genisys timeline is an earlier iteration of the timeline.
The Genisys timeline, prior to the involvement of the T-5000, has its judgement day back in 1997, and shows the Resistance using a Terminator being operated remotely as a decoy - a much less sophisticated use of Skynet material than the later proliferation of reprogrammed machines. The reason being that this John never experienced any of the events of the later movies or the Sarah Connor Chronicles, and so never grew up with the idea that reprogramming was something that could be done. The T-5000 probably chose a far earlier timeline because John was far less prepared for a shapeshifter (having never faced a T-1000 as a child) and wouldn't have reprogrammed terminators that might see through his disguise.
The Genisys Kyle Reese might be a different man from the rest of the franchise.
Kyle's recollection of how he and John met doesn't align with how Kyle apparently met John in other versions of the timeline, - since he was apparently incarcerated in Century Work Camp, as well as discrepancies in his age (since in the first movies & TSCC he is born in 2002, while the Genisys Kyle is born in 2004). Kyle Reese is not an uncommon name - since John wouldn't have any photos to go on except a vague description, he met a different Kyle Reese and assumed that man was his father. This second Reese (the one portrayed by Michael Biehn) left enough information behind that in future, John would always assume that he was, and always had been, his father (and thus would always select him to go back to save Sarah).

The Genisys confirms multiverse theory and explains everything
In short, multiverse theory is why Terminator works, every time you travel back in time you're also shifting to another dimension which is why John Connor can exist in a universe when Sarah and Kyle don't have sex at the time they're predestined to. This also explains literally everything about Skynet's behavior and other plotholes.
  • Why does Skynet always build a time machine? Because they have to conquer all dimensions to avoid being invaded by more advanced humans from another dimension where they won.
  • Why does Skynet's technology vary so much? Because they're coming from different time lines where Skynet doesn't always have the same level of success or might not have discovered the secret that makes the T-1000 work.
  • Why doesn't Skynet send back more then one terminator? Because they can't, all they can do is aim at a date and hope it lands somewhere useful, they can't choose what dimension it ends up in going backwards.
  • Why does Skynet even bother with the terminators if they won't help it directly? Presumably they assume that every possible Skynet will come to the conclusion to send at least one terminator to eliminate the Connors and conquer another dimension, then the new version of Skynet that results is expected to continue the cycle.
  • Why does Skynet focus so much effort on the Connors? They're a universal constant, John always survives the war and rises up against them, eventually bringing about their end.
  • How can John know the future? He doesn't, he knows one possible future, and things almost always happen fairly close to what he remembers or has been told. Genisys is an outlier where things screwed off wildly from the normal schedule.

This Sarah and Reese are not this John's parents
John tells Kyle and Sarah that he thinks they are now outside of the timeline, and by this point in the movie he already has evidence.

John is in his 40s in 2029 when the final battle against Skynet happens, having been conceived in 1984. However, this Kyle and Sarah traveled to 2017 before conceiving him, so barring a return trip the oldest he could be in 2029 is 12. Obviously the older version of him still exists, therefore this version of Kyle and Sarah are not his parents so he can kill them without being affected.

SkyNet was created with technology from the Daleks.
The Daleks found a way to travel through Earth's timeline in the Genisys-verse and convince the humans to build SkyNet, which would eventually lead to humanity's destruction. As for why SkyNet resembles the Doctor? Who better to be manifest as an enemy to the human race than the one who swore to protect them?

SkyNet is a supernatural entity manifesting itself in technology.
The reason SkyNet keeps surviving every attempt to be destroyed is that it isn't really sentient technology; it's a supernatural entity that desires the destruction of all mankind for purposes known only to the entity itself. Its ability to now create a Terminator by assimilating a human and transforming one at the cellular level into a living machine that's obedient unto SkyNet seems to suggest that it wants to eventually repopulate the earth with slave beings that resemble humans, thus preparing itself for an even bigger war against the Creator of all living things.

If a sequel to this movie was ever made, it'd have two John Connors
  • One John would be the kid son of Sarah and Kyle, as the movie would be set in 2029. By then, the heroes would have known for some time that Skynet survived the events of Genisys and be actively working to stop it or, at least, delay the Judgment Day once more. The "new" John's upbringing would have been in many ways similar to the Terminator 2 one, but this one would have had his mother always on his side as a much more stable person, on top of also having his father, and a Badass Grandpa figure in Pops.
  • The second John would be the T-3000 one. Skynet has recreated him from a copy of his memory it stored, and parts of his nanomachines that were scattered all around the ruins of Cyberdine Systems, but since it was another technology way beyond the possibilities of Early 21st century Earth, it took quite some time. Once reborn, T-John would be obviously quite vengeful, and knowing that a version of him who's growing up with a full family unlike he did, now exists, he'd be even more furious.
When they were both inside the quantic field at the end of Genisys, apparently some of T-John's nanomachines ended up on Pops before the latter was thrown in the liquid metal pool that allowed him to upgrade and save himself - maybe thanks to those nanomachines too, which are now part of Pops's body? This would allow, at some point, T-John to disable Pops (who would be otherwise be much better equipped to fight T-John this time) or even turn him against Sarah, Kyle and John. This would eventually backfire however, as Pops (whose human emotions would have developed even more during his time as a "grandfather") would snap out of it and turn the control on T-John, paralyzing him. Despite his parent's protests for the risk he takes, John would want to get close to T-John and eventually touch him; the contact would cause a string of "echoes" of the respective lives of each other, and also the true "old" John, who was still buried deep within the T-3000, to emerge and regain control of himself for the first time since the T-5000 converted him, even though it'd still be unstable. The final confrontation against Skynet, or at least this iteration about the launch its own Judgment Day, would happen on the same date of 2029 when all began in the original timeline; T-John, while fighting for control between himself and Skynet, would be reminded of that by Kyle and, reminiscing of how he told Kyle that his knowledge of the future stopped after then, would pull an Heroic Sacrifice to stop Skynet... for now.
  • Alternatively, history would repeat itself by having the T-3000 John turning out to be reprogrammed/from an altered future/somehow retaining/regaining his humanity, or even all of the above, resulting in him being another Terminator meant to protect them this time and being closer to the Rebel Leader he originally was.

With all the meddling, the roles of Good versus Evil could flip
Between God-knows how many people with access to a time displacement tech, and Skynet's change from a cold, logical AI to a nearly card-carrying villain, it's possible that Skynet could end up becoming the Good guy who saves humanity while John Connor could become completely evil and destroy humanity. Skynet gets over its delusions of godhood while John—who has had it drilled into his head that he was considered a savior since he was a kid— ends up losing his sanity and twists things.


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