It was Ms Hawking, who we’d seen previously in “Flashes before your eyes” and it appears that she has her very own personal Dharma station in the depths below a church, where she’s using this big magnetic pendulum thing, an ancient computer (like in the Swan), and a bunch of complex mathematical equations to help Ben get those that left back to the island.
Charlotte finds out about the discovery of the Flight 815 wreckage while in Tunisia (where the polar bear was found). Based on the timeline of events on the island, and the Find 815 ARG the wreckage was found approximately in early December 2004. Why was there a Dharma polar bear in Tunisia, and why did Charlotte seem to recognise the Dharma logo? Both are questions for another time.
In “Through the Looking Glass”, as the communication room filled with water Charlie wrote “Not Penny’s Boat” on his hand and pressed it against the window for Desmond to see. Then in “The Beginning of the End”, Charlie appears in a one of Hurley’s hallucinations, but this time when he presses his hand against the glass it says “They Need You.”