I've heard two theories about Alfred:
1.) Bruce will fire him/force him to take time off
2.) He'll be killed.
Both of these ideas are being talked about because of Julias' role basically being to fill in for her dad. I have a third option: Alfred has a mental breakdown which could make him into a temporary villain. Why? Well DC loves to bring back old stories and he was turned into a bad guy in the far past. If not then he'll have a normal breakdown after he realizes what he's done and after all the stress has piled up. Think about what he's been through and done.
Jason dies. Bruces' "death." Damians' death. Dick's "death." Having his hand chopped off. All that has to have built up. Now he's obsessed with keeping Bruce in the dark about his Batman life including his family. It's a sham that can't last but he seemed determined to futility attempt to do so. Alfred doesn't even stop pushing untrained kids towards danger after one of them dies! Something has to give and Dick coming back wasn't it. Now Robin War might have the official Robins supporting Alfreds' Robins.
If not then something big has got to happen. More deaths of Alfreds' recruits? Possible but he's not nearly as close to them as the family. If it has to do with the Dick, Jason, Tim and Damian then it'll have to affect their solo titles. Damian seems the most likely since he won't be in BaRE for awhile for unknown reasons. Does he get hurt?
There's also Tim and Jason who are going to have a forced death match. I don't see actual death but that doesn't mean their not affected by it. What if they almost die because of a mistake Alfred made or protecting his team? It might take longer than that if Alfred's going to lead WAR for awhile but something has to happen to snap him out of this. I'm hoping we don't have to wait until Bruce returns to the cowl.