Daenerys has been MIA in Meereen so far in Season 6 of Game of Thrones, but understandably so. She had the Dothraki to deal with as well as building her army, but in "No One" she finally made her way back to Meereen. Dany has been trying to determine the difference between being a ruler and a conquerer lately, tending to err on the side of the latter. But what will Daenerys do in Meereen now that she's back?
Dany has been busy leading her brand new Dothraki army and giving impassioned speeches from atop a dragon, a.k.a. her favorite hobby. When she finally showed up back in Meereen, it was something of a surprise but also characteristically perfect timing on her part: Tyrion and company were under siege from the masters of Meereen, and Dany arrived in the knick of time to help them out. However, she might take issue with how Tyrion has been running things in her absence.
One of Daenerys' biggest decisions as a ruler involved freeing all the slaves in Meereen. This endeared her to the common people and to those she freed, but it enraged the masters and other ruling parties, resulting in the emergence of the Sons of the Harpy. In an attempt to quell the violence, Tyrion set up a deal to phase out slavery over the course of seven years. This went against Dany's decision in a major way and might cause friction between the two.
Tyrion was trying to broker peace in a very Westerosi kind of way by making a deal that he thought benefitted everyone: the masters were calmed and slavery would still be gone. Eventually. However, as Missandei pointed out, seven years is a very long time in the life of an enslaved person. It also goes back on the promises Dany made to the people, which will definitely not help gain their support.
The conflicts in Meereen, while not always very thrilling, have made it clear that Dany struggles to rule even though she excels at taking things over. She very well might leave Meereen to someone else to rule as she powers through on her way to Westeros, though it seems likely that she and Tyrion will have some kind of argument over how he has handled things while she was gone.
Daenerys left a city in trouble and returned to find it in even worse trouble. Finding a way out of this situation could prove Dany's skills as a ruler once and for all – or prove she has a lot more to learn.