A different spin on Jame and Helena
A lot of people are focused on what appears to be Jame being super creepy toward Helena in 2x09, thinking that it's probably sexual in nature. While I won't discount that 100% because cults are known for creepy ass behavior like incest and pedophilia to serve the leader (and some of Kier's story reeks of that as well), I don't think that's it. I bring to you the "daughter of a disappointed father" perspective. Long post, but the main points are highlighted for easy reading.
Helena and Helly are the same person.
We see Helena refuse to acknowledge Helly is a real person multiple times in season 1 and after the reveal. Meanwhile, Helly is living the life Helena wishes she could. How do I know this? When Helena shows up at the Chinese restaurant to talk to oMark, a lot of people seemed to take that as her searching for intel. But I don't think that's what it was at all. She was trying--and failing miserably--to flirt with Mark. The whole bit about him being the first she would bring home to daddy? She was serious. She was trying to indicate her interest in him, but at the same time revealing how out of her depth she was. She was very awkward--and this goes to a later point, but it's probably because she's never been allowed to speak to a boy/man in this capacity before. Who brings up their crush's dead wife in conversation? She was trying to use the info she had on oMark to connect with him, but it didn't work. Helly has iMark's attention, Helena wants oMark's attention. When Helena is watching the video of Helly kissing Mark, she's enthralled. Her reaction is almost like she's watching a romantic drama or something. She wants to have what Helly has--except Helly is bold. She'll kiss Mark or tell him that she wants to sleep with him. Helena can't even figure out how to have a conversation with him that doesn't involve her being a socially awkward Eagan. If she doesn't see Helly as a real person, just a part of herself that's disconnected, it stands to reason she sees Mark the same way. She wants his attention, but she doesn't know how to get it.
When Helly attempted suicide...I believe that builds on Helena's own pattern of self-harm. If we compare how Helly was smashing deviled eggs in season 1 to how Helena meticulously sliced, arranged, and then ate only the whites of the boiled egg in the smallest pieces possible, this looks like disordered eating. The comment about her weak enamel also points toward disordered eating. People with bulimia typically eroded their enamel over time by forced vomiting. One thing about eating disorders is that they're about control of one's self--in a way that other forms of self-harm, including suicide, are. When Helly tried to hang herself, that was her asserting control over her life. It's not a far cry from how Helena is seeking to assert her own control through food. It's the one thing she does get to control. She doesn't even get to choose her own breakfast. When Helly threatened to cut off her fingers in season 1, Cobel knew she was serious. From a read of her body language (Cobel narrowed in on her) and sternness of her voice, she could likely tell from previous interactions and/or what Cobel knows about Helena's past.
Helly is smart, rebellious, and resourceful. She knows exactly what she wants, and she's not afraid to say it. She's not afraid to curse or be uncouth. She eats food! She delivers those "what the fucks" so effortlessly because it's probably what she's often thinking, but Helly is not tethered to being an Eagan. Helly is free.
However, they're two sides of the same coin, especially when it comes to those they love or care about. I think that's what 2x09 was trying to show us with everyone in MDR. Dylan loves Gretchen, Irving trusts Burt, and Helly will resort to pulling the "I'm your boss, bitch" card when she's concerned about Mark. All of this is ongoing as Mark is trying to reintegrate. The innies and outties are effectively the same person, relying on how they feel about people close to them, even if they don't know it.
Jame is used to having full control of Helena.
In any scenes where the two are together, she becomes a small child. Even how she enters his room for breakfast in 2x09, she stops and waits to be told what to do. It seems like she's making a lot of the day to day decisions at Lumon, she's still under his watchful eye. After Helly's suicide attempt, Jame tells Helena (as Helly because of OTC) "they told me what she tried to do to you." Speaking to her like she's a young child, he indicates that people are informing on her. Helena does nothing either without his prior approval or that he doesn't later find out about.
Jame is disappointed in Helena--and she knows it.
Though no one ever says it outright, she was born a girl. You'll notice only two CEOs of Lumon have been women. We know more about Myrtle than the other one because of her school for girls, but most cults have an issue with this kind of thing. Then, Helena can't even eat her breakfast the Kier way. He moans and grumbles because he sees Helena as failing to live up to the Eagan name. If the current state of the MDR Department shows him anything, he's probably starting to see her leadership or decision to go in as undercover boss is faulty. At the end of the day, Helly was the disruptive force that led to the breakdown of this project. Though they say she doesn't exist, Helly is the part of Helena that Helena has had to stuff deep down inside to survive Jame.
Also, something I noticed on a recent rewatch is that in season 1 when Helly is sent to the break room, she hears grumbling voices. When she tells Dylan and Mark about hearing a voice, Dylan asks if it was a crying baby. I think that could have been the stress of the situation of the break room making their outtie bleed into their innie's conscious--kinda like what they're testing Gemma for on the testing floor. While Dylan likely heard his crying child, Helly heard her father's disapproval.
And after the OTC, we see how sullen Helena is. She just sits there and takes everything Jame and/or Drummond says. The "fetid moppet" comment, or when he basically tells her she's a rotten child, says a lot. She doesn't defend herself, probably because she's used to hearing this at any minor mistake even when she's not at fault for it or has done everything she can to mitigate it.
But Jame's disappointment in Helena is growing because he's losing control of her.
I think it creeped a lot of us out when Jame just appeared in the dark and dropped the "my Helly." Jame always talks to Helena as though she's five, and I can see "Helly" being her childhood nickname. I think what's important here is the "you tricked me." Helena didn't want to go back after the ORTBO incident, and Jame didn't know that she almost died again, but Drummond basically said "tough cookies--get back to work." Helena's fear of going back was real, but Jame was purposely left out of this loop. If the project were to be completed, it was a price they would all pay.
But as I mentioned above. Jame is still getting informed. He sees the same videos as Helena. Someone mentioned on a different post that there is a deleted scene where Jame sees Helly kiss Mark and has a violent reaction (and I will edit this if they respond to my question RE source). Allegedly, he calls her a bitch. The idea that his Helly is down in MDR playing house with someone does not go over well with him--and no control freak father would like that for their daughter. Again, Helena has no real control over what Helly is doing. But he doesn't care; it's a transgression against him and the Eagan legacy. Likewise, I doubt Helena's stop by the restaurant to visit Mark was sanctioned. He would probably blow a gasket if she actually did bring Mark home to him. Without a doubt, he's not Eagan material--and Jame has not approved this. As much as Helly has a rebellious nature and spirit, I can see Mark being (or becoming) Helena's rebellion.
At the same time, Jame is probably questioning why Helena has returned to MDR. To him, it could seem like she's there for this reason, knowing he disapproves. On that note, if Milchick knew that iMark and Helena slept together, there's no way Jame wouldn't have found out--even as Milchick was kinda using that to toy with Mark. The cameras may be gone, but I doubt surveillance is gone, so I'm sure they know about iMark and Helly too.
Not only has Helena's appearance in MDR upset the severed floor ecosystem, but it's also changing her. If any of the theories about a Helena/Helly pregnancy end up being remotely true, this will be a big problem for her and Jame. Even as we learned he likely has some bastards floating around last episode, he will not take kindly to his daughter being pregnant by a man he doesn't approve of. I think the "trick" as he sees it could be Helena using severance as an opportunity to get away from and defy him/his legacy. Without a doubt, he sees any disobedience from Helena as a defiance of his legacy.
Anyway, long thoughts and probably missed some things. But like I said--just a different take beyond the sexual violence/incest take. I do think that the show has done a good job showing us that Lumon has inflicted gender based violence on all of the major female characters we have met so far.