* Claire took extreme offense in "Raised by Another" when referred as "crazy" by Charlie. She had a similar reaction to Hurley when someone referred to him as "crazy". As a teenager, Claire couldn't deal with the sudden impact of finally meeting her biological father, surviving a fatal accident and her Mother being in an induced coma of which Claire thought she was the cause. She was admitted to a psychiatric hospital and whilst there, met a man named Thomas. They were released from the hospital around the same time and continued their lives together. The reason Claire took such an interest in Thomas was because all he did during his time in the hospital was paint therefore Claire knew how important Thomas' painting was to him.
* The testing that Others where doing on her while in captivity were fetility experiments. They took blood samples from her and gave her vaccinations in The Staff.
* She was meant, along with Aaron, to be a part of the Others' genetics/fertility-related experiments.
o This has been proven to a degree, given that they were analyzing Claire to see if they could find a cure to their own fertility issues. And Aaron is probably the first child born on the island since Alex, and there is no indication whether fertility had become an issue when she was born or whether the Others were simply unable to capture and analyze Danielle before she gave birth.
Death theories
Is dead
* Claire is dead (allowing for the idea she may be "dead" in the same sense that Christian Shepard is dead). She did not die at the barracks. Hurley, Sawyer, Locke et al have been interacting with and possibly touching her (definitely touching in Sawyer's case her) since the RPG round hit her house. She suffered a blow to head in the explosion and then was very disoriented. Sawyer commented and said "she got her bell rung but she'll be fine." After that, when asked how she was feeling, she said she had a headache but was fine. Victims that have had head injuries often feel fine but then later they have brain hemmorage and it eventually kills them. It is a symptom of severe concussions.
o Claire does die (technically) from belated brain hemmoraging in Something Nice Back Home, but her body and soul are subsequently restored by the island similar Christian. At that point, Jacob sends Christian to escort Claire to The Temple (leaving Aaron behind in the jungle), where she later projects her image to Locke in the cabin and to Kate off of the island. This happens because the Island has decided that Claire "still has work to do" and is important to protecting the island.
* Claire's last nurturing act as a mother is to feed (nurse?) Aaron, and lie down with him for the night. She dies, is absorbed by the Island and "awakes" to find Aaron apparently missing but actually in the arms of his grandfather, Christian. Together, they find a safe place to leave Aaron where Sawyer is sure to find him and leave for their ultimate meeting with Locke at Jacob's Cabin.
* Miles' interest in Claire is based on the realization that she is about to die. He asks to carry Aaron because this is his first experience with pre-death and he does know what will happen when Claire crosses over(dies), and he doesn't want Aaron to be dropped and killed.
* Claire is dead, having died in the barracks when the mercenaries blew up her house. Why the others could see her is unknown. Perhaps it was the islands will. This explains why Miles was so interested in her. Wondering why, since she was dead, everyone (including herself) acted as if she were alive. Knowing she was dead, Christian Shepard went to her. She wanted to take Aaron with her, but he explained that she could not and convinced Claire to leave Aaron where the others could find him.
Is not dead
* Claire is not dead. The reason why Miles was acting strange was because he could sense Christian near her and wanted to carry Aaron as a precaution.
* Claire is not dead. Locke is dead and now taken over by Jacob's nemesis. Claire was forced to give up Aaron, as Jacob's enemy needs him for something. She tells Kate (through her dream), "dont you dare bring him back." This was so Aaron can be protected off-island from Jacob's nemesis.
edit In the Future
* She will be reunited with Thomas and Aaron and they will be a family. Thomas left Claire for the same reasons Desmond left Penny (for noble reasons, to be reunited in the end with her), and this will become apparent to all later on. This also explains why Thomas was, at first, ecstatic about having a child, and then suddenly wasn't.
* In Kate's dream, when Claire tells her, "dont you dare bring him back Kate" she is not referring to Aaron. She is referring to Locke. Claire is dead, or at least in the same physical state as Christian, and being controlled or used in a similar manor. Claire says this know that if they bring Locke's body back to the island, Jacob's nemesis could inhabit it and become a threat.
Jacob's Cabin
* Christian led Claire to Jacob's Cabin in order to keep her safe from the Kahana mercenaries. Christian did this on behalf of Jacob, since he (and the Island) would not let Claire die as she is the only one who can raise Aaron, stated by Malkin.
* When Christian first met Claire he was much kinder to her than we ever see him being to Jack. This is why he lead Claire to safety.
* Jacob's nemesis, posed as Christian, brought Claire to the cabin in order for her to break the circle of ash that was placed to keep him out. Claire followed because she thought that she was following her father Christian.
edit Desmond's Flash
* Desmond's flash about Claire getting into the helicopter with her baby did not happen because Charlie died. Up to that point, everything Desmond saw in his flashes happened besides Charlie's death. As far as we know, only part of what Desmond said to Charlie happened (the yellow light went out, and Charlie died).
o What Desmond saw in his flash will come to pass and Claire and Aaron will be rescued in Season 6. The events that Desmond saw just haven't happened yet.
o Desmond lied to Charlie. He say himself getting into the helicopter/ being reunited with Penny, and told Charlie he had seen Claire get onto the helicopter so that Charlie would die an Desmond would get off the island.
o Desmond actually saw Kate getting on the helicopter with Aaron, he thought it was Claire.
o Claire is the loophole that Jacob's nemesis talked about. By making sure she wouldn't leave the island the other chain of events started. He did see Claire get in the helicopter. So far Desmond's flashes have all been extremely accurate in detail, with the exception that he changes details by saving Charlie, but in the end he couldn't prevent it.
Pregnant on the Island
* Claire's collapse in "White Rabbit" was the beginning of the "side-effects" of being pregnant on the island. This is how Ethan realised that the same thing that happened to women who conceived on the island was happening to Claire. Ethan then began injecting Claire with the serum after her collapse.
* Ethan only took Claire to make sure nothing happened to her baby. They did not know that a baby could be born on the island at all. Claire had no side affects on the island because her baby was not conceived on the island. Women who conceived on the island had different problems (dying during the second trimester). Her fainting was a side effect of exhaustion and heat mixed with the fact that she is pregnant.
