Why was only Lucifer in the cage? Where is Michael?

That is an excellent question. I know no definite answer and I fear it won't get resolved just like other plotholes (The Colt for example, where the hell did it go?? Many situations where this little thing could've saved the day). My thoughts when watching this episode:

• Michael is dead, killed by Lucifer inside the cage after Sam got saved because the two archangels had nothing else to go on. Theoretically Michael is stronger but Lucifer didn't retreat when the 1vs1 was closing in so he saw a reasonable chance to win over Michael.

• The cage got damaged, Lucifer could reach out and also pull Sam inside. Maybe he can do more. And maybe Michael can do much more. Maybe Michael could get out when the cage got damaged while Lucifer was either unable to or tried to get his true vessel the sneaky beaky way. Michael's more naive world view would explain why he didn't show up yet: instead of doing something on his own, he's trying to find Daddy.

• The small version of the cage Rowena set up is merely a window to the true cage. So not the whole stuff inside gets transferred, the enchantments made only Lucifer visible - like when calling a number and only one person of a household answers (Lucifer knew the call was coming as he set it up).

I have no more reasonable speculations, I hope it will get resolved soon. That episode was one hell of a plot twist. Sry for bad English btw - German.

It's either a plot hole (annoyingly, again..like with Adam).. Or I also agree about it only being a window to the cage, but then when he's inside why didn't it revert back with Michael? Maybe it will.. This could be a great opportunity to resolve the Adam plot hole. I hope they don't screw it up. I'm getting tired of with the length they've been on air with the increasing number of plot holes. They need to find a way to end it on a good point and wrap up plot holes.

At the end of the episode, when the darkness killed some of the angels, we saw clouds gather and a beam of light strike the darkness, we presumed it to be God. This; however, could have been Michael, and he could have escaped when the darkness was released. We saw that other archangels have power over nature, such as Raphael with lightning, and Michael was shown to be able to control the light when Adam was seized. Not to mention that Michael is essentially the crown prince of heaven, and would be inclined to defend his subjects.

Sams' visions of the cage always showed it suspended by chains in mid air surrounded by darkness. So if thats the real cage, then what we saw in that episode must have been the "window" thing. although i was let down when michael was absent from the cage. You would think thats too big of an oops for the producers to miss, so i choose to believe all will be explained. If not, well it wont be the first time we have to say 'oh well' in this series and move on.

If I recall correctly, shortly after the darkness is released, some of Crowley's demons report to him that they heard a scream coming from the cage. It is specifically discussed that either Michael or Lucider is trying to warn them of something. So, they acknowledge the ongoing existence of Michael at least up until the early part of the season. And, we know that something significant happened in the cage at that time, significant enough to cause either Michael or Lucifer to cry out, although we don't know what that is. It is also specifically stated by god that “Michael is in no condition for battle” he implies that he is still alive. (Said while they gather Crowley and Rowena to fight the darkness)

Maybe Micheal and Lucifer made a plan to get sam knowing dean would try to come rescue his brother and then they have both there true vessels in one place and a ticket out of the cage. And Micheal is some how hidden right now and goin pop out from no where