Sail to The Reaper's Hideout (located at I-12 on the map), and inside a tent on the southeastern side of the island cluster you will find a representative of the Reaper's Bones named The Servant of the Flame. Talk to him and purchase the emissary flag for 20,000 gold. Then turn around and vote to raise your emissary flag on the table next to you (and ask others in your crew to vote for it as well if you aren't playing solo). As soon as the final vote is locked in and the flag raises on your ship, the achievement should pop. (For me it was instantaneous.)
Note that you cannot already be flying another emissary flag or you will be unable to vote to become an emissary of the Reaper's Bones. If you forgot to cancel your existing emissary flag before leaving the last outpost you were at, you will need to head back to any outpost and cancel their emissary flag from there before voting to fly the Reaper's Bones flag.
Hope this helps! If you have any questions, please just ask. Happy sailing!