But wouldn't they die if they lost their Biju, so the Kages would have to fight without them.
Bee yes... Naruto no. His mother was capable of surviving.
Anyways.... if they lose their Bijuu... here's my take.
Naruto will be somewhat comatose... due to just losing Kurama. Most of the alliance will fall into despair, but I imagine people closest to Naruto (K11, Go-Gokage Rangers, Sasuke, Hokage) will try to rally people to keep fighting as that's what Naruto would do (the cheesiness and all of its glory).
Sasuke losing his "best friend" or maybe the fact he didn't finish Naruto himself will give rise to his Perfect Susanoo or if he already has that a new Sharingan technique.
The Kage will get the motivation to kick it up against Madara. Honestly I think at that point all of the Hokage would be gone except maybe Hashirama... so really they were irrelevant in my above comment.
I'm guessing around this time they'll go to make a final suicide charge, when in steps Orochimaru and Kabuto with that poison capable of weakening the Shinju Tree (Stopped Yamato). Sasuke, Orochimaru, and Kabuto would take on Obito... Manda II would bite the tree poisoning it (weakening it). The alliance under Shikamaru tries to find some strategy despite little hope.
Meanwhile, the Sage and Naruto may have a talk in the Bijuu Subconcious... Naruto having been stuck there while losing Kurama (hence his coma like state... not to mention a weakened body). Basically the talk would explain some more history stuff... the whole Chakra origin needs to be discussed. But when it comes to finding a solution, the Sage will tell Naruto he has to find this for himself... as the Sage could only delay the Juubi, but never truly solve the problem.
Likely after that we'll have Naruto wake up.... pulling out SM, and then with the aid of the alliance making a path for him... he'll get to the tree and try to save Kurama.
My guess is the Fruit will bear once more, and despite his efforts Madara won't get to it in time... Naruto will, but he'll smash the fruit instead of eating it. Possibly causing some unexpected plot twist..... IDK!
At that point it gets into even worse speculation than I'm already at... but I guess if Naruto loses Kurama he'll go back for him, and that likely means either becoming the Juubi's host, or finding some way to force the thing to split itself once more.
That's the best I can do.... maybe Kurama gets re-sealed, but I imagine the Bijuu go free if they are released. Impossible to REALLY say.