After finishing the second stage and entering the portal to the final stage of the final boss, the boss takes damage, but the joining allies timer starts, which teleports you back to the second stage where you can take the portal to come back and do some damage before you are again teleported back because of joining allies. After killing the boss, the joining allies timer eventually teleports everyone to the second stage, but the portal is closed with no way to the final arena where the chest would spawn, so you can't complete the mission.