NCIS/WMG

Jenny Sheppard's plot line is not over.
Jenny was killed off, true; but we never found out the story behind her father. Isn't odd that, just as she was looking into him and had evidence that he was still alive, someone from her past magically finds her and kills her? The timing is suspicious. Whatever she was involved in isn't over yet.
 * And we never see her dead body.
 * This was apparently a request on Lauren Holly's part - her sons watch the show - but that doesn't mean they can't use it for plot purposes.
 * Thus, since we didn't definitively see her dead body, and we didn't see how Vance, Ziva, and Tony processed the scene before Gibbs arrived, perhaps there was a cover-up. It's not hard to imagine that Jenny wanted to fake her own death so that she could do her own investigating without the burden of another investigation into her activities as director. Perhaps moments after "Judgment Day Part I" faded out, Jenny sat up and explained things to Ziva and Tony, and gave them a big SHHH.
 * And Mike Franks is the only person who knows Jenny's current whereabouts. Maybe.
 * Didn't Jenny have a terminal illness and not long to live anyway? It was stated several times during that season.
 * Ducky's in on it too! Because Jenny knew she couldn't hide her preparations for going underground from Gibbs, she distracted him with pretending she was dying of a fatal illness. We never DO find out what she's supposed to be dying from, and Ducky would have handled the autopsy personally like he did for  so no one else at NCIS would actually know.
 * So, basically, what we have here is NCIS as a whole creating a conspiracy and leaving Gibbs out of the loop. Surely he'll be calm and understanding when he finds out.
 * This has been the plot of many a Jibbs fanfic. No, he doesn't take it too well.
 * Jenny's dead, and that's her eyeball. Now tell me, is that her father's Roaring Rampage of Revenge, or Jeanne Benoit's?
 * We do see her body, in the reflection of some glass. She's dead.

NCIS has a serious mole problem
We've caught one mole, but there have been several times when various other agencies have taken long hard looks at NCIS for moles, both before and after the resolution of the 'mole plotline.' There's still at least one mole in the organization. == In the last season or two of NCIS, the show will move away from its 'realistic' take, and feature a shadowy organization that was behind much of the earlier plot twists, including Jenny's death and Mossad agents tendencies to go rogue. == We'll only find out about it after Eli David is rousted from Mossad and the agency falls under the evil organizations power. Said organization is probably connected to whoever Jenny Sheppard's father works for.
 * It's not a heavily publicized federal agency In-Universe. That might make it easier for a mole to get top secret intel once they burrowed in.
 * And now the Los Angeles branch has been compromised: someone found out Callen's real identity and copied all of their case files from their mainframe. They seriously need to update their security protocols.
 * Well there was that whole Riley McAllister thing. He wasn't exactly a mole but he was definitely a traitor and he was there for ages.
 * There must still be a mole, because in "Pyramid" Tony is given a mission to flush out a suspected mole.

Rivkin's apology just before he died in Aliyah was not for dying, but for betraying Ziva.
And he was drinking so much for the last few episodes of that season because he did not like betraying her.

Allison Hart didn't show up because Bell sent her; she got Bell off on her own.
She'll turn out to be related to Shannon or one of Gibbs' early cases somehow, and is bent on revenge. But will instead wind up in love with him.
 * I second this theory. She seemed much too personally ****ed at Gibbs' entire method of investigating for it just to be because her boss told her to.
 * And now that she's showing up in cases that have nothing to do with her boss...
 * As a follow up to the above. Allyson Hart will have a 'My God, What Have I Done?' moment in the season finale or in the build up to it, and end up working for NCIS next season. She'll be the Cuddy Character to counter-balance Gibbs.

Tony was once a foster brother to Temperance Brennan
Seems to be a popular fanfiction idea. Tony has mentioned a sister multiple times, despite being reminded he's an only child. Also, Bones was in the foster system for what seems to be quite a while, it's not impossible that at some point she was in the care of the DiNozzo family. Besides, the DiNozzos are rich, they could probably handle a foster kid or two.
 * There is another link between both series: Booth is the nephew of Gibbs. Based on the fact that Gibbs' father and Booth's grandfather are played by Ralph Waite playing practically the same role. Gibbs can't be Booth's father because Booth used to be beaten by his dad and Gibbs would rather kill himself than hurt a kid.
 * Also, that warehouse manager from "One Shot, One Kill" is the long lost twin brother of Jack Hodgins. Sibling Yin-Yang is in effect because the warehouse manager has a lot more faith in the FBI than Hodgins does.
 * This crossover would have to reveal that Cam has been in the witness relocation program, since she used to be NCIS agent Cassie Yates...
 * If FOX and CBS ever team up they could explore this under the guise of a murder at a Mystery Writers convention. After all both Brennan and McGee are writers. Heck, ABC could get in on the act and add Castle.
 * I dunno about Castle, but Bones and NCIS seem to be just begging for a Crossover.
 * I'd vote to throw Castle in the mix. They could be doing a joint book signing, which is how they meet, and then... Yeah, I'm going to stop before this stops being a theory and turns into a fanfic outline.
 * Feel free. Meanwhile, this troper will simply sit in awe of the potential of David Boreanaz, Mark Harmon, and Nathan Fillion all leading an investigation together.
 * I actually saw a prompt like that on the BBC Sherlock kinkmeme, with the addition of John Watson, of course. Sadly, it was prompted over a year ago and never filled.
 * Well, since Angela's dad recently appeared on CSI: Miami...
 * By that argument, one could claim that both CSI: Miami and Bones are non-fiction, as Billy Gibbons exists in Real Life too.

It's the same boat.
Whenever Gibbs finishes building it, he takes it apart and starts over. Why does he do this? Because he uses boat building in much the same way as other people would use model trains, or bonsai trees. It acts as a way for him to work off the stresses of the day.
 * Where does the wood go?
 * Storage.
 * Apparently the one named Diane just got lit on fire.
 * Jossed by the fact that he gave the Kelly to Mike Franks.
 * So he gives away his finished boats (or, if he can't find a person to take it, throws it away) because he has no interest in it after he finishes the construction?

NCIS-LA's missing agent Dom is actually a spy/ManipulativeBastard.
The kidnapping is just a cover for him to return to whoever he really works for (they had to be really realistic just in case his car was bugged), and the next time we see him he'll be gloating over the Evil Plan he's pulled over the whole team.
 * Or, if he's not already a spy, if/when he's rescued he'll be suffering from a bad case of Brainwashed and Crazy, More Than Mind Control, or possibly just some Laser-Guided Amnesia.
 * This entire theory is Jossed...* sniff*

NCIS is actually an alternate universe for the Stargate Verse.
Let's face it, the sheer number of former Stargate actors appearing in the show cannot be an accident.

Kate actually ascended.
She's not ascended! She's a reaper.
 * She's not a Reaper! She's immortal.
 * She's not immortal! She's the Undead.
 * She's not Undead! She's actually dead.
 * She's not Angelic! She's still dead, though.
 * She's not that dead! She's still very dead, though.
 * She's not even that dead! But she is dead, though.
 * She's not that dead either! She's just a little dead.
 * She's not even really quite dead! Just a little.
 * She's been dead for ages! But she never let that stop her.
 * She's not dead and she never had been! Because she was never alive in the first place.
 * She regenerated after being buried and escaped from her grave!
 * She didn't die at all because she's been in witness protection and got a job as a medical examiner.

Abby's going to die in the season finale.
Something major is going to happen, anyway.
 * I personally think she'll die at some point.
 * Not that it's going to stop her...

Abby's right.
Gibbs really IS a bit psychic.

Gibbs's Rule Number 34 is the same as ours.
Because... because... because Why not?!
 * Because McGee would be the only one to get the reference, except maybe Abby. Not that Tony would need to get the reference.
 * Who said it had to be a reference on Gibbs's part?

Tim is bi-curious.
Tony seems so adamant!
 * Hmmm, I wonder why?

Gibbs got the boat out of his basement by using magic.
There is no other solution - even Abby remained stumped.
 * He went the Salem Academy, the American magic school in the Potterverse.
 * No, Gibbs broke the bottle. Just like those ships in bottles....Wait...that would mean that Gibbs took his house down. Yeah, it's not the other kind of bottle breaking that is revolved around ships.
 * Alternatively, Gibbs fixed the boat with his most piercing glare and simply intimidated it out of the basement.

Gibbs's mother was a redhead.
Hence his attraction to them. Also, his daughter Kelly was a redhead, so she had to get the redhead gene from both parents. Jackson Gibbs did not have red hair, as seen in the episode "Heartland", so it had to be a grandparent from one side of the family at least.
 * His mother, grandmothers, great-grandmothers. All it actually requires is having a redhead SOMEWHERE in the family tree.
 * Perhaps, but this theory is that it was his mom.

Gibbs' mother was deaf.
He knows sign language for no readily apparent reason. We know his father isn't deaf. There's never been any sign of any other close family members even existing. Seems to make sense.

Further to this, in a Much Wilder Mass Guess, Gibbs may have inherited the condition that made his mother deaf, based on his statement, when asked if he was deaf or stupid, that he's "a little of both".

Vance will be killed or somehow removed from the director's position at some point.
Now that we've learned his big secret, about the page he took out of his file, his big background event is resolved. When Jenny Sheppard's background event was resolved, she died. Based on precedent, it's not looking good for Leon...

McGee's mother was Gibbs’ mysterious redheaded girlfriend during the first two seasons
He did not know she was dating Gibbs until he saw her at the office and asked Tony and Kate what they knew about her to see if they were aware of his connection to her. He did not reveal he was her son because he got the job on his own and was afraid that his co-workers would tease him about it like they do about everything else. Finally the two of them looked quite a bit alike (the actress who played her, Vivienne Bellisario, is the real life mother of Sean Murray who plays McGee).
 * Don't think so. In the first chapter where McGee sees the mysterious redheaded woman, he asks who she is.

Gibbs will retire in the series finale.
The final scene will be McGee hazing the new agent, and Tony will come up behind him and give him a Gibbs Slap.

Gibbs will die in the series finale.
The final scene will be Gibbs in the afterlife reuniting with his family.

At some near-future we will have CGIS spin-off show.
Hardly WMG, methinks.

The eyeball belongs to Agent Keating
His teammates on the brief "new team", Langer and Lee, both turned out to be important and Keating did nothing. Now it's his turn to be killed by the plot.
 * No, the eye has been confirmed as belonging to CIA agent Trent Kort.

The File Tony was handed in the finale of Season 8
Was either about Ray or Kort. It's clear that those two are part of some new mystery, and we can pretty much rule out Gibbs or McGee as people who would betray their country.
 * ...it's almost certainly about Agent Mitchell, who was the leak.
 * I'd say the leak is, given that   Hence Tony's reaction to the file, seeing as
 * Jossed,  In between Seasons 8 and 9, Tony will have

Season 9 will be the last
Something will lead to Gibbs deciding to finally retire for good this time, but will have likely solved some massive conspiracy. Of course, a flash forward will show that Tony and the gang still call to him much like he did with Franks.
 * Unlikely, given the ratings. The only thing that would stop the show now would be one of the main actors leaving (and even that could be covered, as we saw with )
 * Jossed, just got renewed for season 10.

Gibbs is a wizard.
You know it's true.

When we'll find out how Gibbs get his boats out of his basement...
...we will find out for what G's name stands for.
 * Nope. we know what the G stands for now. The boats are still a mystery
 * Huh? When did we find that out? I didn't see that in the newest episode! Either I missed something or you are very misinformed.

Gibbs is the goddamn Batman.
He got the boats out via the Batcave.
 * While he could possibly be Batman, he most certainly is not the Goddamn Batman, since he isn't a hobo named Crazy Steve.

The agent Tony is tasked with investigating at the end of Season 8 is on his own team.

 * McGee or Ziva more probably than Gibbs, but nobody is ever above suspicion. If it is one of these, they will likely turn out to be innocent, however. Another dramatic choice would have been Barrett, but she left.

Jenny bought Mossad information on The Frog with putting Ziva on the team.

 * Jenny clearly had few rules she wouldn't break in her quest to get The Frog. As letting someone she knew and trusted on the team would get her good information on The Frog so she could set up her op in a year or so, letting Mossad have an agent inside NCIS was a fair price in her mind.

The UST between Ziva and Tony shall be resolved on the Series Finale

 * The writers know that Tony and Ziva's UST is one of the biggest subplots that has helped them keep their viewers as the seasons have worn on. When it comes time for them to hang up the towel, they'll put Ziva and Tony together to satisfy the shippers and the final gray-out of the series will be Ziva and Tony sharing a kiss.
 * So they're making Tony and Ziva the Harm and Mac of this series? That actually makes a lot of sense. Both Harm and Tony had many interests who went bust. They also had a relationship which ended with the death of the woman they liked. Ziva, like Mac, enjoyed a few relationships with similar guys. Both had a relationship with a non-American who loved them and went to great lengths for the, Mic the Aussie and Michael. Both then moved onto a CIA man, Clayton and Ray. I wonder if they will debate on who will quit by flipping a coin like in the JAG series finale.
 * It is hinted rather heavily that the UST between Tony and Ziva has been resolved quite a while ago, and that they are just keeping up appearances. It doesn't break this theory, but it will soften the emotional impact if the ending is "they were a couple all along, but they just kept it a secret."
 * But the obvious reason they AREN'T an explicit on-screen couple is because the writers know the Will They or Won't They? of Ziva and Tony's relationship is a big contributor to the great character dynamic of the show, and they'd risk Shipping Bed Death if they resolved it before the end of the series.

Abby is a Spark.

 * Abby's ability to produce massive amounts of incredibly precise forensic evidence, in record time and on her own, is due to her having the Spark. Her eccentric personality and her suprising ability to hold her own against violent opponents are other indicators. Forensic science and computer science are her scientific fields of choice.

There is an in-universe show about a fictional NCIS team
And it started about the same time as the real show did. That's why, after the first few episodes, hardly anyone ever asks who/what the hell NCIS is when the team flash their badges at civilians. At some point, the navy consultant attached to this show will be murdered, and Team Gibbs will be called in to investigate.
 * The episode in question will have a large amound of meta-humor. And McGee will have to go undercover as his "Gemcity" persona again to get into a famous person party.

Ducky is Illya Kuryakin

 * Illya Kuryakin was the cover identity of a young British doctor-turned-MI-6-agent named Donald Mallard. He was exposed as a spy in the mid to late 1960's, though his actual identity was never revealed. He subsequently retired from MI-6 and went back to his medical career, eventually becoming the medical examiner at NCIS.
 * Gibbs tells Kate in the Season 2 episode Meat Puzzle that Ducky looked like Illya Kuryakin when he was a young man, but it's never explicitly stated that Illya Kuryakin was a character on a TV show, so, in-universe, Kuryakin could have been a well-known exposed spy.
 * Ducky's history is largely a mystery, so, really, it's possible.

Gibbs gets the boats out
By wishing them to the cornfield.

Ray Cruz was a fall guy for the CIA

 * He fell on his sword so to speak, to cover up the fact that the agency was perfectly ok with Ray's assassination attempt on U.S. soil. Allowing the agency to disavow all knowledge of the assassination. Alternatively the agency turned a blind eye to Ray's rouge tactics as long as he didn't get caught. When he killed the lieutenant by accident the CIA washed their hands of him.

Gibbs is a Jumper

 * It's how he gets the boats out.
 * It's how he catches up to every bad guy by taking the long way.
 * It's how he moved from the hill where he sniped the terrorists to the building, about half a mile away, in twenty seconds.

Tony and Ziva both took the bed in Paris

 * They'd already slept in the same bed before, so the awkwardness probably wouldn't be that high. Telling other people though might cause unwanted attention of Did They or Didn't They when they probably didn't for the viewers' sake of keeping up the UST.
 * Since they both asked why the other lied at the end of the episode, it is heavily implied that they shared the bed.

Gibbs is the Angel of Death

 * The show already has elements of Magic Realism, and there are just some things about Gibbs that just can't be explained away by Memetic Badass.
 * The boats. He gets them out with his powers, and he does carpentry as a Homage and to experience creation rather than destruction.
 * The fact that his gut is always right, even when all the other characters have been wrong at one time or another. He already knows who the murderer is in any given case; he just can't let it be known until proof is found.
 * Being able to cross a mile in less than two minutes without any fatigue- in a desert, clad in full combat gear, carrying a sniper rifle, while being over the age of 50.
 * He became the Angel of Death after taking his revenge for the deaths of his family. The position is an acknowledgement of his will to protect people and punishment for the sin of taking judgement into his own hands.
 * Gibbs is grooming Tony and/or Ziva to be his replacement once he moves on.
 * Ducky knows what Gibbs is and helps him keep it hidden. Why else would a cornor be one of his friend? They're co-workers in a company besides NCIS.

Shannon and Kelly are not dead.

 * Season 3 was the first season where hints about Shannon and Kelly were revealed. In the Season 3 episode "Bait," a Marine's wife was being hunted by a drug lord because she had testified against him, leading to her faking her death and going into hiding. This is eerily similar to what happened to Shannon: She was going to testify against Pedro Hernandez, but he ended up sniping the agent protecting her and Kelly, leading to their car crash. In one of the flashbacks in "Hiatus," Franks shows Gibbs the car which was carrying the Gibbses, but we never see their bodies, only their graves. The real question: if they're not dead, did Franks, Jenny, Leon, etc., know?

Gibbs
I can't think of any other way I think he would find more preferable.