This was one of the best dramas I watched.

Everything is good, the acting, the soundtrack, the story...

It gives us action and intrigue in equal and healthy doses and even in it's most slow and calm moments it keeps us enthralled in the story.
The actors are brilliant and convey their emotions as if we were there with them and the soundtrak wraps everything perfectly...

That being said, I know many watchers got confused by that ending, BUT:

The script writer left for the audience to think about what happened...

Now, I personally think they had to be apart for 3 years by Emperor's decree in order for her to be redeemed and for him to fully focus on his task, and in the end, three years later, when both had done what they had to do, they were allowed, as a reward, to reunite and to live their lives together...

And the coup of poison was in order to fake her death like she did during her execution in early episodes...