- Max and Eleanor's breakup. From Max begging Eleanor to choose her over power and Nassau, to Max realizing she won't and demanding that if Eleanor's going to screw her over, she at least admit it out loud, the whole thing is just heart-wrenching.
- Gates' death. After a season of slowly losing his faith in Captain Flint, his friend, when Flint's small fleet comes up against a Spanish man-o-war, Gates can't take any more of it. He tells Flint that he's going to have the pirate ships turn around and return to Nassau, at which point Flint will be deposed. You can tell how much it destroys him to betray his best friend, but he sees no other choice when it becomes clear that Flint is going down a dark path. Then, Flint kills him, and it utterly destroys him to do it. Flint, who has spent the entire season in a cold, simmering rage, breaks down crying and apologizing.
- The reveal of McGraw's relationship with Thomas Hamilton. The two were lovers, and when they were found out, their relationship was made a travesty when McGraw was expelled from the Royal Navy and from London, and Thomas was institutionalized, at which point he killed himself.
- The very broken way in which Captain Flint introduces himself to Abigail Ashe. She guesses at his name, thinking she knows who he is, and he replies "My name is James. James McGraw." in a way that it seems he's not only saying it to her, but to himself.
- Miranda's death. Just as she and Flint come close to having their dream of a Nassau free of pirates seems to be coming true, Miranda puts two and two together and realizes that their friend, Lord Peter Ashe, was the one who betrayed them all those years ago in London, resulting in McGraw's exile and Thomas' death. When she, justifiably enraged, decries him for a coward, a hypocrite, and a traitor, she's shot by Ashe's henchman, Colonel Rhett. Flint's reaction is heartbreaking: impotent rage at the destruction of the final vestige of his old life.
- Muldoon's death. He was, at that point, probably John Silver's closest friend on the Walrus, and the two of them are below deck patching up holes from cannon fire while the rest of the crew tries to get the ship through a storm in one piece. When the ship tilts strongly to one side, Muldoon's legs are crushed and pinned by a cannon that came loose from its moorings. And the water is still rising. Silver spends the next few minutes trying in vain to move the cannon. As the water levels get higher, Muldoon talks to Silver about how people say dying isn't so bad, that you get to see everyone you love again, but it's clear he's just trying to comfort himself in his last moments. Then, he goes under, and he starts flailing and crashing around as he starts to panic, and all Silver can do is scream as he tries and fails to pull his friend above the water. When Dooley finds them, Silver is just staring blankly at his dead friend.
- The death of Charles Vane. After making peace with all his old rivals, Flint, Jack, and Anne, he is captured by Governor Rogers and hanged by Eleanor in Nassau's square. While at first, the crowd jeers and throws fruit and vegetables at him, once he is given a chance to speak, and tells the people of Nassau that they have the power to rise up and throw off English tyranny, and then faces his death without an ounce of fear, the crowd grows silent and looks disgusted with itself. The worst part, though, is that for all his dignity going to his death, Charles is still human. Once he steps off the cart and the noose tightens around his neck, he manages to remain still for about ten seconds, but after that, he starts to panic, twitching and jerking at the end of a noose. Despite all the horrible ways to die this show has given us, the very worst is seeing a great man twitch silently as he slowly chokes to death. It gets to the point where a trio of pirates walk up to his body and pull it down, forcing the noose tighter and ending Charles' suffering quicker.
- Various character's reactions to the aforementioned death. Teach is the first to find out about it, and when we see him as he meets with Jack and Anne, you can tell that Teach, despite generally being stoic, has obviously been crying. For Jack and Anne's part, as soon as Teach confirms their fears that Charles Vane has died, their faces tighten up in pained anguish. The exchange between Jack and Teach perfectly encapsulates how much Vane's death hurt both of them, and how angry they are about it:Teach: "Charles is dead. The Governor in Nassau hung him in the square, on the island I helped to build. He thought he could do that and face no consequences. He failed to account for me."
Jack: "British laws sentenced him, but I think you and I both know who it was that fashioned that noose; it was no 'he'. I look forward to seeing Ms. Guthrie again and settling Charles' account with her."
- Jack positing that, if Charles was a son to Teach and a brother to to Jack and Anne, there's some kind of connection now between Teach and Jack and Anne, even if he isn't sure what it is. For his part, Blackbeard seems to treat Jack and Anne with more gentleness and respect that one would expect, indicating that he's aware of some bond, as well.
- The death of Teach. After the crews of Rackham, Bonny and Teach lose a battle, they are captured. Rodgers proceeds to have Teach keelhauled. After Teach survives the first attempt, they do it again. After he survives THAT attempt, they do it again. Teach being Made of Iron, he survives that attempt as well and Rodgers proceeds to just shoot him through the head.
- Not only that, but because he held on for so long and undermined Rodgers' intended message, Jack was spared the same fate. Teach may not have been able to secure his familial legacy with Charles, but at least he got to save the next best thing.
- In the series finale, John Silver's and Flint's final scene together. Prior to it, during a brief exchange between the two of them and Jack Rackham, Flint began to suspect that both Rackham and Silver were plotting to kill him once they retrieved the treasure Flint had buried earlier. Silver instead offered Flint a choice, either give up his war or die. For all of Flint's machinations and the number of people who were either betrayed or killed because of them, it's genuinely heartbreaking to see how hurt he was by Silver's perceived betrayal. It's likewise very clear that, for everything that's happened between them, Silver still considers Flint as a close friend and is only doing what he feels he must to protect Madi, even if it means killing Flint, no matter how much he doesn't want to. In the end, Silver manages to convince Flint to drop his war against England, as it's revealed that Thomas is indeed alive and well. The two even end up reunited through Silver's efforts.
- That's if you believe Silver's story. There's enough potentially wrong in it (matters of timing, which Madi herself bring up, for one) that it's possible that it could just be all a lie. And that he really did kill his friend to save the woman he loves.