After you helped Ineffa recover her memory in Natlan, both of you undertook a long journey to Nod-Krai, which was not easy at all, but after all you had a mission. Once you were in Nod-Krai, the first thing you did was take out the letter that Varka had sent you through Ineffa. In his letter he said that Nod-Krai was not going through a good time, basically a confrontation, war, between different factions, such as The Fatui and the Abyss Order, Varka's letter also said that you should look for him, in a tavern known as "The Flagship."
You started looking for the tavern that he mentioned in his letter with the help of Ineffa. After a few minutes you were already in front of the door of the Slavic-style tavern... you were already there, you just needed to find Varka inside.