Mother returns to the caves at night where Jacob is sleeping. She wakes him and tells him "It's time." She leads him through the jungle and as they're walking Jacob says that "Something happened, didn't it?" She tells him that she had to let MIB go because she doesn't have a choice and it's what he wants.
As they reach a stream, she asks him if he recognizes where they are and he does. It's the stream that leads to The Source, the tunnel of light. She passes Jacob the torch, literally, and tells him that he must protect The Source now.
Jacob asks what's in the tunnel and Mother says that it's life, death and rebirth, the heart of the island. She tells him to never go down there because what will happen would be much worse than death.
Mother then pulls out the bottle of wine (the same one from "Ab Aeterno") and a cup. She chants in Latin was has been deciphered as "Nam non accipimus hoc quasi vulgarem potionem, sed ut ille sit quasi unus mecum." That roughly means "For we do not accept this just as a common drink, but as if that (he?) should be one with me."
She pours some wine into the cup and tells Jacob to Drink. She says that if he drinks, he accepts the responsibility of protecting the island as long as he can, and then he'll have to find his replacement. Jacob says that he doesn't want to protect the island. She says that someone has to and Jacob says that he doesn't care. She says that her time is over and it has to be Jacob that takes over.
Jacob gets emotional and says that he doesn't have to be him because she wanted it to be MIB, and now "I’m all you have." Mother says that it was always supposed to be Jacob and she sees that now and one day he will too. She adds that the doesn't really have a choice though, so he must take the cup and drink.
Jacob reluctantly takes the cup and drinks. Mother then takes his hand and says "Now, you and I... are the same."
So we see that Mother essentially forces Jacob to take the role of protector of the island. She says that he doesn't have a choice, which likely led to Jacob's view that everything is a choice, which he told Hurley in the back of the cab in "The Incident." Jacob has always seemed to push people in a certain direction, but never forces them to do anything. Jacob seems to do many things differently as the protector of the island.