Wildmore/Eloise and MIB are in the same side. Why? Because several things that have happened in favor of MIB and against Jacob had been caused by Widmore or Eloise:
- Widmore was expulsed from the Island. According to what we know, that happened because Charles had a relastionship with someone outside the island (and Penny was born). But who expulsed Widmore? Ben and the Hostiles -> Richard -> Jacob
- Widmore sent the Kahana freighter to the Island. He wanted to find the Island. But Ben, leader of the hostiles, didn’t want Widmore people in the Island. In that moment Ben and the hostiles followed (or tried to follow) Jacob instructions given through Richard. According to what Ben said to Locke in season 4, Widmore wanted to exploit the Island, but maybe since that time what Widmore wanted was to help MIB to go out from the Island.
- Eloise said to Jack that he must go back to the Island in Ajira 316 and that he had to take something belonged to his father. Jack put Christian shoes in Locke. Maybe that has something to do with the fact that MIB take the John Locke shape. Remember that before we watched MIB in season 5, Christian was the character nearest to the smoke or maybe Christian was the previous MIB body.
- Eloise wanted Desmond go back to the Island in Ajira in season 5, but Desmond didn’t do it. Maybe, she wanted to save transportation cost that later Widmore had to pay to take Desmod to the Island in season 6.
- But why Eloise wanted that Oceanic Six go back to the Island in AJIRA? I think that maybe to help MIB to find the loophole in what he was going to kill Jacob using Locke shape. Or maybe, also to take 4 of 6 candidates (to replace Jacob) with MIB so he could recruit them (Jack, Sayid, Hurley, Dead Locke). In this point is when I think that Jacob entered the picture and allowed Jack, Sayid, Hurley to travel in time to 1977 (Kate was just a scort to motivate Jack and Sawyer)
- Well, returning to the Eloise/Widmore alliance with MIB, I think also that maybe they manipulated to Daniel Faraday (their son) to provoke the Jughead explotion and so help to create (in that moment or later in 2007) the alternative timeline. Now, in this new timeline, Faraday has repented because he knows that it is not what was supposed to happen. Or maybe, the purpose of Jughead explotion was the death of Jack, Sawyer, Sayid, Jin and Hurley (remaining candidates to replace Jacob). And in that case maybe Jacob helped them again to travel in time to 2007. Remember that everything is about a Backgamon game, where Jacob and MIB have checkers (black and white stones).