Last we see of him, seastone-handcuffed by the Marines lead by Issho.
And based on the spat between Issho and his boss Sakazuki, I'd say Doflamingo should still be under Issho's custody, not yet handed over to Marine HQ.
So what fate should befall upon him now?
- Death (be it swift execution there and then or judged execution or any other likes of similar) is highly unlikely, given the track records of One Piece and author Oda and with the great character development he received thus far, he seems to be too interesting and good a character to have met an end in the series as yet.
- Thrown into jail? Impel Down perhaps? The betting chances is there but I don't think so. He knew too much politically, as such it may backfire on the gorosei geezers should Doflamingo start to blackmail with whatever leverage he had over them. The hype is there about what he knows, thus I think it may be too significant and critical a piece of something (knowledge, material, etc) that is worth its weight over the WG., as such does not deserve something as simple as imprisonment.
- Be pardoned and set free? May not be possible after what Issho's broadcasted prostration. People are now aware of who Doflamingo was and what he did (not sure by how much but ASSUMING all the tyranny in Dressrosa as well as his illegal underworld dealings), so public perception of the Marines will deteriorate even further should this option occurred. Sakazuki seemed to care about Marine's "credibility and trust" a lot, this I'd think he will have issue and object strongly should this come to pass, that is IF he can do anything about it.
- Pardoned and reabsorbed back into Tenryubito status? Wild idea and highly unlikely but who knows... In this case, public perception can be muzzled simple because he is now a World Noble and World Nobles are Gods. But with his now tainted background, I doubt Tenryubito will want such a person in their status, a rotten egg in the basket. Plus I think Doflamingo is not the type to sit all day and idle around without much happening going on.
- Think this may be the most plausible one, escape captivity to survive and live on as a pirate. Again, I am under the assumption that he is still under Issho's custody, so trying to break free may prove to be difficult. But if there be even a small bleak of hope, my bet is on Sugar and her Hobi Hobi ability and its side effect. Should Sugar be able to be free from her seastone cuffs, she can turn Doflamingo into a toy, thus erasing his presence from memory, escape from Marines custody with her small child physique and at a safe location (on or off Dressrosa) return her master back to human form. What he does after escaping is another topic altogether (independent or join a yonko).