We saw Whidmore arriving at the end of Dr. Linus, not stopping at the beach where Jacob’s team is hanging out, but moving on to their original destination, where ever that may be.
I don’t think Whidmore is coming to the island to join Smocke or jacobs team. In the episode Ben and Alex were discussing the 1813 Charter Act which essentially gave control of India into the East India Trading Companies hands.Â I think Charles is coming to the island with similar intentions. With the backing of Whidmore Industries that has ties to the Hanso Foundation and Paik Industries he is going to try to stage his own coup on the Island. Not realising the battle that is forming between the two factions that are on the island already.