It would seem that after uploading Micro Super Defense Force a month or two ago, I failed to notice in all this time that Duel Mode still had a playtesting shortcut that took people directly to the final boss instead of fighting each enemy one by one like it's supposed to.

So, if you played the game already and were like "...wtf?", that's how it happened and you can enjoy Duel Mode as it was meant to be now. If you played Micro SDF recently, you may have to erase your browser history to view the new version. Playing it on a different browser also worked for me.