Rousseau meeting Jin later and not recognizing him is OK
Rousseau never talked to Jin directly before the time-shifting and so never realized it was the same person. Jin was already on the raft the first time Danielle comes to camp to "warn" everyone about the Others. Jin was then with the Tailies for a long while. Jin and Danielle never came face to face, even briefly, after their time-traveling encounter. Therefore, there would be no Danielle not recognizing Jin, because she doesn't see him again.
When Rousseau was watching Claire and the rest of the camp at night she was no doubt assessing them. And she did at least see Jin during her walks into the camp. However it is possible that her decrease in mental health and the number of years made her not remember his face as she seems to not recognise Ben as the one who stole Alex.
Rousseau's interaction with the Others
When she caught Ben, she must have recognized him as the man who took her daughter. At the same time never tortured him, never interrogated (unlike Sayid for example), she just took him to the Losties saying that he was an Other. Quite a weird behavior for a woman who was deprived of her new-born child and who was looking for her daughter for 16 years.
From the main Rousseau page: "She says the baby was taken by the Others but she also has said that she had never seen one of them at that time and only knew them as whispers." Given Rousseau is obviously mentally unstable, she could have convinced herself her child disappeared rather than face the idea she let her be taken.
She was always very clear about the fact that "one of them took my baby".
Another wierd thing is her transmission. The Others must have known about it, but for some reason they let it play for 16 years.
Why would they remove it? The Looking Glass station was jamming all transmissions anyway, so her signal was doing nothing.
Rousseau apparently arrived on the Island in 1988, but Goodspeed's ghost says he's been dead 12 years. Locke was talking to Horace's ghost in 2004, so the purge happened in 1992. Danielle avoided "the others" on the island, and was possibly living in the part of the island belonging to the 'hostiles', which is why she never seemed to have any direct contact with the Dharma Initiative or vice-versa.
The terms of the Other/Dharma "truce" was that the D.I would vacate the Island after 15 years. It was signed in 1973 so I would assume the Purge happened 15 years later, in 1988.
The DHARMA Initiative was active on the island until December 19, 1992, the day which the Purge occurred, NOT 1988!
Rousseau never was infected, she just went insane over having to shoot her entire crew, her baby being kidnapped, etc. Claire only bears resemblance to Rousseau because she has had to live on her own for 3 years, so she has learnt some survival skills. Claire is still infected and 'serves' for the Black Monster now.
They were both infected. When we've seen Claire with Christian in the cabin, she was alright with missing Aaron and whatsoever. She hasn't looked alike Danielle at all. The only thing that can fight the infection are motherhood feelings (Harry Potter, anyone?). At first Claire was OK with joining Christian, but then she started to miss Aaron, freeing herself from "the darkness". Danielle was caring about her child all the way through it.
We have always automatically assumed Rousseau was "good" as she helped the 815 Survivors against the Others and subsequently took her word that her team was infected. The time-flash where Jin sees her team attempt to shoot her seems to make this seem true. However, the team members try to tell her that the Smoke monster is the "security system" for the island, which turns out to be true, as when Ben summons the monster to stop Keamy's team, the heiroglyphics were translated to mean "To Summon Protection." The fact that Rousseau's team knew of the role of the smoke monster implies some interaction with the Others, who we know are on the side of Jacob. The fact that they tried to kill her might mean she was really the infected one as we do not know what the cause of the infection is directly, and there was also a time lapse between when we see her team pulled under the temple and when she faces off against them. It also stands to reason that Claire has fulfilled the Rousseau role, setting traps for the Others and antagonizing them. Between Dogen's remarks that Claire had turned evil AND her presence in the ash-circle cabin with Christian Shepherd (Smoke Monster) it is highly plausible, that Rousseau was in fact bad all along. In the season 4 episode entitled "Beginning of the End" she sides with John Locke's team, the consequences of which lead to the Oceanic Six leaving the island (which we obviously know is against Jacob's wishes, as he attempts to bring them back but does fit into Smoke's wishes of John Locke dying). Our automatic assumption that Rousseau was good and the Others were bad isn't necessarily the case and our point of view might need to be shifted to Others = good, Rousseau/Claire = infected and working with Smoke against the others.
Rousseau clearly was the one protected by the Island in her fight against the bewildered French team. It wasn't she that was infected, it was her husband(?) when he was about to shoot a helpless pregnant woman carrying his daughter. It is not reasonable to assume she was 'evil' at that time. IT is VERY reasonable to assume the french team was 'turned' evil.
The monster-controlled members of the expedition tried to kill Rousseau, which leads to think she wasn't infected ... her pregnancy might have protected her.
Rousseau was infected
She perceived her teammates as 'sick' and 'infected', but it was in fact her who was infected. When her teammates entered the temple, they were persuaded that Rousseau had been claimed and needed to die. They were sent to kill her, just as Dogen sent Jack to kill Sayid.
Rousseau became a killer through this ordeal, just like Sayid. She also became insane over time and obsessed with getting her baby back, just like Claire.
Was she still a part of the science expedition in the alternate timeline?
She was, but everything went according to plan.
She wasn't, they never went on the expedition.
Will be paired with Ben. Her need for a caring husband/father figure and Ben's daughterly love for Alex will lead to this.
The expedition was intended to reach the island
She may have been sent by the Dharma Initiative to find the island, using the their station under the church.
Could Jacob have possibly gathered the group (like the ajira group, but not knowing about it).