Alex Rider/WMG

Alex can easily blow MI6 to pieces by going to the media
Whether he will is another matter, but...

Sure, he signed the Official Secrets Act. But he signed it as a minor, under duress. Any lawyer will tell you that the only way a contract under such circumstances would be of any use to anyone is if it were printed on toilet paper.

They could ask him to re-sign when (or if) he turns 18; in the meantime, it might be wise to pay him more and give him a hand with the chronic schoolwork issues.
 * But then wouldn't MI6 have him arrested or sic their 00 division on him? And they're blackmailing him, using Jack's expired visa. If he says anything to anyone, Jack will be sent back to America, and he'll be forced to go to an orphanage. Yet again, this troper doubts that MI6 could still blackmail him if Alex went public with the truth, but it's still something to consider.
 * "Hello, my name is Alex Rider. I'm not even 18 and my life is SO AWESOME that you want to print it. MI 6 has a child spy program, like on that kids show, but it's real and I'm in it. My uncle was a spy and he taught me and the housekeeper to do martial arts, skiing and kill people with blowfish. I've been in space, and I've saved all the schools from the Prime Ministers chronies, and I killed this black guy who was turning white. Give me money!
 * It's made obvious in Crocodile Tears he doesn't want the story to go to the media, because then he'll lose whatever he had of a normal life and become an international celebrity.

Alex died fighting with his clone in Point Blanc
Just think about it. The way he coldly walks away from the unconscious body as it's about to be engulfed in flames. The way he pushes Damian Cray into the jet turbines. The way he feels happy when Nile is incinerated - maybe it reminded him of the death of the original Alex?
 * But isn't that impossible? After all, clone-Alex's main objective was to continue his father's work, to become the most influential person on the earth. Why would he waste his time with MI6? Wouldn't he have tried running away and finding ways to accumulate wealth rather than work with a spy agency?
 * Wealth is not the only way to get influence! And MI6 is a powerful spy agency.
 * True... but then how's a kid supposed to control MI6? Does he inherit it when Blunt dies?
 * But he couldn't possibly have fooled Jack (especially since Alex wasn't even disclosing his real name in Point Blanc).
 * Besides, he had memories of his previous adventures that had a massive impact in later novels (like Scorpia and Snake Eyes). There's no way the clone could have access to them.
 * Alex had already displayed somewhat psychotic tendencies. Almost murdering a drug dealer, anyone?
 * That was accidental - he intended to put the dealer's boat in the police station car park, but someone switched off the crane's power supply before he could get it there.

Alex is a young James Bond
Ignore the Celebrity Paradox. Imagine Alex growing up to be an incredibly skilled secret agent, but also a disillusioned womaniser who barely cares about his job.
 * Wouldn't he have to go back in time to be James Bond?
 * He's also a Time Lord.

The original Alex Rider died in Scorpia
In Point Blanc, we see the perfection of cloning technology for humans. We're expected to believe that the government didn't take advantage of this in any way? Perhaps either they: - Found a clone/clones that hadn't been subject to plastic surgery from Point Blanc - Created their own clone of Alex from scratch and artificially induced ageing - Found and treated the actually-alive Alex clone from PB - Or, created a clone, induced him into a chemical coma until he aged correctly

Of course, they'd need a way of planting false memories so the clone didn't realise, but in the latter case, perhaps they developed that while he was out, and he's simply made to believe no time has passed. (It'd explain why we go from 2000 to 2009 tech between Stormbreaker and Crocodile Tears without so much as a year passing...)
 * Jossed by Ark Angel - in the opening chapters, Alex is recovering in hospital and Horowitz explains how the bullet didn't kill him.

All of the events in the books are fabricated by MI 6.

 * Alex Rider is being trained to be the ultimate agent, but is not actually participating in real hazards at this point. They are all fabricated incidents whose purpose is twofold:
 * 1: Train Alex. Make him ruthless, increase his skills, and get him used to the life


 * 2: Render working for MI 6 his only choice for a career. With all the time Alex has spent missing school, he's fallen dramatically behind in his schoolwork, he'll eventually fail as the trend continues, and without a basic education, his only hope for a job will be MI 6.


 * Whilst this is pretty much Jossed by the end of the series (several scenes with Mrs Jones and Alan Blunt make it clear this is not the case), Crocodile Tears suggests that the two theories may be valid to an extent, as Blunt says they'll have to make sure they recruit Alex full time.

All of the villains that Alex goes up against are very sick people.

 * No, not that kind of sick (although I suppose that's true too), but sick in the head in such a way that every single one...and I mean EVERY. SINGLE. ONE! suffers from an irresistible compulsion to spell out his or her plan in minute detail, outlining exactly what their goals are and how they intend to accomplish them, practically giving Alex all the information he needs in order to beat them on a silver platter. Seriously, how did these people meet with any success ever?
 * Alex is only a kid, so MI 6 only pit him against mentally ill criminals. Sane criminals are handled by the adult spies.

The invention in book 9 will be a suicide pill.

 * Apparently, Word of God says that there is an invention made by Smithers that has appeared (without us noticing) in every book to date, and it will be used in book 9. In Spy Fiction, agents tend to be equipped with a suicide pill in case of impossible odds or some such. So, to give us a Downer Ending or possibly a Deus Ex Machina, Alex will either take the suicide pill or give it to someone else.