Ilana was there to deliver what was in the box (John Locke's body) to Jacob. We also learned that Jacob had visited Ilana in a hospital in Russia (Ep: 5x16, The Incident). Her face was all bandaged. Jacob apologized for taking so long to visit and asked Ilana to help him.
When she learned of Jacob's death, she sobbed and said that he was like a father to her. How did these two meet? What is their history? Why was Ilana in bandages? There are so many unanswered Ilana questions.
- Ilana’s world was turned around when she learned of Jacob’s death at the hands of MIB and Ben, and with Jacob’s death Ilana lost Jacob’s insights that would have helped her in her tasks. Ilana, like Ben, was one of many of Jacob’s soldiers who were sacrificed by Jacob for his own purpose. Ilana and Ben felt that they had a special connection with Jacob, but he hadn't felt the same.
- Ilana was Jacob's daughter, though she didn't know it. He had allowed her mother to leave the island and Ilana never knew her father until he sought her out when she was an adult. Without telling her they were related, he recruited her to help him.