Darth Chronus said:
Well by the time the Executor exploded into the Death Star II, the shield was down by then and the Emperor was thrown down that shaft by Vader - so the duel would have been over.

It could be some other kind of explosion like an additional rebel ship blowing up perhaps.

What about the Death Star's superlaser?

Since it's never really established in the film where the Emperor's tower is, it could be within view of that.

I'd bet the Emperor's inner Michael Bay would love to have a first-hand view of whatever the DS is blowing up, and it's firing away at the rebel fleet while the duel is going on.