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Ok I have been like 85% sure Prometheus and Helix are in league but after last night’s episode, despite what some people have argued, I am now 100% convinced. There are too many patterns involving Prometheus and Helix that are too coincidental for there to not be a connection.

Adrian reports a Vigilante sighting after defeating him

How do we know this wasn't planned preciously to fuel Felicity's drive to find him, thereby leading to her freeing Cayden James to further his own plans?

So in last night’s episode Adrian goes missing and nobody, not even A.R.G.U.S. can find him, yet Helix has a special technology that can track someone’s heart? Yea didn’t buy that for a second. Yet only if Felicity helps them spring a dangerous hacker and after doing so she gets the alleged technology only for it to be a disguised EMP. How do we know Prometheus didn’t stage all of this? How do we know he didn’t want Cayden James out of A.R.G.U.S. to further his own agenda? It was argued in a previous post of mine that Helix can’t be in league with Prometheus because they exposed him to the world but what if that too was part of his plan? I think Adrian deliberately unmasked knowing the camera was there so A.R.G.U.S. would make him the most wanted fugitive in America to push Felicity’s desire to find him leading to what happened in the last episode.

Artemis

Who says Evelyn is the only one Prometheus intends to corrupt and turn against Oliver?

Prometheus claims to be 10 steps ahead and has done little to prove he isn’t, and for a guy who has spent the duration of the series watching and studying everyone in Team Arrow to such a fine detail you don’t think he’d account for quite literally the smartest woman on Earth? I think Prometheus wanted Felicity to join Helix from the start to fuel his own agendas and to torment Oliver by turning his former lover against him by corrupting her mind with grief, making her easy to manipulate. I should also add Prometheus did promise to turn everyone against him as he did Evelyn so why shouldn’t that include Felicity?

Felicity Smoak

I think Prometheus has been playing Felicity from the start, knowing that grief would make her easily manipulated.

To this end I think Prometheus had Billy killed to make her angry and then had Diggle sent back to prison thereby setting up Felicity’s meeting with Helix  as she only exonerated John with the information they gave her, and Adrian used this to exonerate John so Felicity will begin to trust Helix more. After a taste of what they can do he then kidnapped Susan not just to torment Oliver but to force Felicity to resort to Helix again, after making sure Susan couldn’t be found by their usual methods, so long as she took down a homeland security drone to further his agenda. At the same time he also deliberately unmasked on a rooftop knowing Helix would catch the footage and Felicity decoded it thereby giving her more reason to trust Helix. Then Adrian becomes the most wanted man in America who nobody can find so Felicity agrees to help Helix free Cayden from A.R.G.U.S. in exchange for the technology to track him, thereby giving Adrian what he wants and instead sends an EMP to the Arrowcave. Now they're trapped and while Team Arrow tries to rescue them Prometheus will probably be setting up the next phase of his endgame. Most likley Adrian is plotting to destroy a city to prove a point and Felicity will be the one to blame as her pursuit of vengeance led to her repeating Havenrock all over again.

Billy Malone

Having Billy killed has allowed Adrian to ruin Oliver's reputation in numerous ways, not just to torment him. Because of that I also think it was to manipulate Felicity.

I don’t think manipulation like this is impossible as Adrian has done it to Oliver. Manipulating him into killing Billy didn’t just torment him but it also allowed Adrian to force Oliver to label his alter-ego as a villain, thereby giving Adrian a scapegoat for his own murders which only further discredited the name. I’m also still convinced that Dinah is in Star City because Prometheus used Earth-2 Laurel to motivate Oliver into keeping his promise to Earth-1 Laurel, thereby giving him a sense of hope Prometheus intends to rip away. And yes despite knowing that Dinah is main cast for next season I still don’t trust her, not Eobard Thawne distrust more like Earth-2 Harrison Wells distrust. I think Adrian is holding her family hostage, based on exchanges between him and her in 5x15, and she’s an unwilling spy.

So yea I'm convinced Prometheus has been behind all of Helix actions, at least those relevant to his own agenda, and given how stupid Felicity has become, allowing the ends to justify the means and becoming a Malcolm Merlyn in the making, it wouldn't surprise me if Prometheus has in fact been manipulating her this entire time.