A pivotal plot point was contained in the episode "A Tale of Two Cities."
Jack, Kate and Sawyer have been captured by the Others. Unknown to them, they have been taken to a secondary island, Hydra, and held in cells (Jack inside the facility and Kate & Sawyer in outside polar bear cages).
Jack wakes up in a holding cell. He sees chains across the ceiling. He seems to be on some kind of table. He looks at the inside of his elbow, which has a band-aid on it where something had been injected or blood given. He tries to open some kind of hatch/door but it is locked. Some kind of electronic device used to "communicate" is on the wall, but it does not seem to work. Jack sees another door on the opposite side of the room, but when he walks toward it he collides with a glass wall blocking his way. Water is dripping from the ceiling. Jack tries to break the glass, unsuccessfully. He shouts for Kate, but there is no reply.
Kate wakes up in a bathroom with "Mr. Friendly," Tom, standing over her. He indicates a clean towel, a new bottle of shampoo and an unwrapped bar of soap, and tells her to take "a nice hot shower." She refuses to shower in his presence, but Tom laughs and tells her she's not his type; he then leaves. Kate sees that she too has a band-aid on her arm.
Sawyer wakes in an outdoor zoo cage. He looks around and sees speakers and a big tube with an unknown DHARMA logo. Also, he notices other nearby structures, including a cage similar to his, with Karl inside it. Sawyer tries to get answers from him, but the man does not respond. Sawyer looks around his cage some more and sees a strange contraption/button inside that has a large "button" with a knife and fork painted on it. He tries to figure it out, and pushes the button. A "Warning" sound goes off. Sawyer pushes the button again, the same sound goes off. As he is about to push the button for a third time, the prisoner in the cell opposite warns him not to. Sawyer pushes the button anyway, and receives a painful electric shock.
We learn fairly quickly that Hydra station was for animal experimentation. It is also away from the main island, which adds another level of security and therefore danger to the castaways. Each castaway had been apparently "injected" with something in their arm. We would later learn that Sawyer has a chest scar, as Ben shows him that he is trapped on the island, that contains an explosive device set to go off with high blood pressure. Most people believe Ben was bluffing the con man, but Sawyer believed him enough to cooperate and control his anger and rage to escape.
It is clear that this episode shows the brilliance of Ben's evil mind. He has taken three strong willed survivors and put them into a situation where he can play each their fears, desires and self-interest off each other.
But the key plot point was the beach scene.
After Kate's encounter with Tom, she takes a shower. When she emerges, she finds that someone has taken her clothes and left her a dress instead. She puts it on, reluctantly. Tom and three Others bring her to a beach, where "Henry" is waiting at a covered table with chairs, freshly cooked food, utensils, and coffee, with a pair of handcuffs on the side. He tells her to handcuff herself or she gets no coffee.
She asks "what did you do with Sawyer and Jack?" But "Henry" notices that she started the question with Sawyer and not Jack. Kate asks for her clothes, "Henry" tells her they burned them. When she asks why he's doing all this, "Henry" responds that he gave her a dress to make her feel "like a lady," fresh food to make her feel at home, allowed her a view of the beach because her friends are seeing the same beach, and utensils to make her feel civilized. He tells Kate that he gave all those things to her so she'll have something to hold on to, because "the next two weeks will be very unpleasant."
After some experimentation, and with the help of a large rock Sawyer found outside the cell, he soon figures out the mechanism that delivers food and water. The water streams out a pipe into a trough, kibble falls on the ground as well as a large fish biscuit -- animal food. As Sawyer drinks the water, Tom returns and he puts Kate into the cell that Karl had occupied. He takes off her cuffs. She also has visible cuts from the handcuffs and Tom remarks "cut you up pretty bad, didn't they." Tom, noticing that Sawyer was able to obtain food, first congratulates him, and then mocks him by telling him that the bears figured it out in two hours. Kate is in the cell across from Sawyer's, and he tries to make her feel better by joking around. She seems distraught, so Sawyer asks if she wants something to eat. Kate says yes, so Sawyer throws her a biscuit which she eats pitifully.
And the unsaid aspects of the beach scene hover over the rest of this story arc.
Apparently, if Kate was still hungry upon her return to the cage, then she must have not eaten with Ben on the beach. That would mean that Kate decided not to cooperate with Ben. But what was the proposal(s)?
We know that Ben had risen to power by being brutal and controlling of the Others. But as king, he wanted to solidify his kingdom with a queen. Juliet had refused his romantic overtures, so Ben killed her lover and vowed to keep her a prisoner on "his" island. We could assume that in the beach conversation, Ben made a similar demand: Kate would work with him (or be his consort) or one of her loves would die. When Ben picked up "Sawyer's" name first in Kate's concern, Sawyer got the chest bomb. (Some could argue that was the plan all along since Ben really needed Jack to do spinal surgery on him.)
Ben had all the intel on Kate's past, so he probably used it against her. Criminal minds think a like, and Ben was a master of leverage. He could have used Kate's secrets to claim that he could turn her over to the authorities and receive maximum punishment if she did not cooperate. Kate was always a runner; a person who never wanted to face her responsibility or accountability for her actions. She also had in the past used then discarded her lovers when she needed to keep running from the law. Kate could have decided to cut a deal to "stay" on the island, i.e. to be Ben's double agent.
It would then make sense why Kate demanded to go on ALL the remaining missions. If she was Ben's inside spy, she could tell the Others exactly what the castaways were planning to do. Juliet was a later obvious choice as a triple spy, using Jack's affection for her to get herself into camp leadership and trust roles (as a medical professional helping Claire), but also to balance or confirm Kate's potential spy activities.
The deal could have also been that Kate had to choose between Jack or Sawyer. Ben probably pressed her to choose Sawyer, since he needed Jack to turn his back his feelings on her. And it worked. Out of character, Kate made a move on Sawyer which Jack "conveniently" saw on the bear cage monitors. With Kate choosing Sawyer as her island lover, Jack was heartbroken - - - and fell in line to help Ben.
It would not have been out of character for Kate to sell out Jack by pretending to bond with Sawyer. But like all Kate's decisions, she did not follow through very long with Sawyer (only enough to escape from the Hydra station.) There was conflict in Kate's mind since she immediately started to plan a rescue mission, but it was Jack who told her to NEVER return. When she did try a rescue mission, we saw the shock on her face when she saw Jack playing toss with Tom in the Barracks yard. Jack was suddenly integrated into the enemy camp - - - and he looked happy and content. Kate was shocked - - - and she was taken away with the impression that Jack was lost to her.
At that moment, Kate's "bad" decision in choosing Sawyer over Jack was apparent. It was a decision that would haunt her for the rest of her life. She would only "remember" the pain and deep love for Jack when she awoke her soul in the sideways afterlife. This is the only rational explanation of why Kate would be so clingy to Jack in the sideways church at the End. She got her one second chance to be forever in love with Jack - - - something that would have not happened if not for her "deal" with Ben on the Hydra beach.
