I thought the whole idea of having the portal gems was that it allowed creatures or keepers to reach the surface safely. They've always been able to leave through the heroes doors but not able to survive on the surface in daylight now you have it you can. Maybe the portal gem allows powerful beings like keepers or Horny to have control over the overworld.
I read a good plot wereby after the events of DK2 horny stole all your power and made an atempt to take the overworld and when he was thwarted by the goodly forces he was driven back meanwhile you have been building up power again so that you can atempt to take the overworld for yourself now that the portal gem has given you the ability to spread further. You also have to fight against horny who is now your enemy.












