Warning: SPOILERS Ahead for Arrow Season 5 Finale
The sins of both the father and the son was a driving theme in Arrow season 5. In the season finale "Lian Yu," Adrian Chase (Josh Segarra) and his minions kidnapped the members of Team Arrow to lure Oliver Queen (Stephen Amell) to the deadly island purgatory where so much of Oliver's destiny was decided. Most importantly to Oliver, Chase held his young son, William, hostage. Chase's plan was to make William's father choose between saving him or saving all of his other loved ones trapped on the island. Oliver saved William, but Chase exacted his revenge, detonating explosives all over Lian Yu and seemingly killing all of Team Arrow. But prior to that explosive cliffhanger, a different father made a different sacrifice for his child.
While making their escape, Malcolm Merlyn (John Barrowman) took the place of Thea Queen (Willa Holland), who had stepped on a landmine. Merlyn joined Oliver's rescue team only to save Thea, and true to his motivations, he placed his own life in danger to protect his estranged biological daughter. As Thea and the rest of Team Arrow continued their escape, Merlyn was left to confront Chase's men, including Digger Harkness (Nick E. Tarabay). Malcolm took his foot off the landmine, setting off an explosion that killed himself, Harkness, and Chase's soldiers. With that noble sacrifice, Malcolm Merlyn's story in the Arrowverse came to an end.
Malcolm Merlyn was a legacy character in the Arrowverse with deep ties to Oliver Queen's family. Also known as the Dark Archer, Merlyn was the original Big Bad of Arrow and remained one of the series' very best. Introduced in the earliest episodes of Arrow season 1 (at first known simply as "mysterious businessman"), Malcolm, the CEO of Merlyn Global Group, was soon revealed to be one of the wealthiest and most powerful men in Starling City. Merlyn also coined the name "Green Arrow" at a season 1 Queen dinner party, which Oliver immediately dismissed. He was the father of the late Tommy Merlyn (Colin Donnell), Oliver's best friend, and in season 2, Thea learned that an affair with Moira Queen (Susanna Thompson) meant that Merlyn is her biological father. Later, Merlyn became Ra's al-Ghul, until Nyssa al-Ghul (Katrina Law) dissolved the League of Assassins, which cost Merlyn his left hand. Later, Merlyn was one of Eobard Thawne's prime recruits to join him and Damien Darhk as the Legion of Doom. With the Legion, Merlyn was successfully able to recreate reality itself, until they were foiled by the Legends of Tomorrow.
Though his avarice and nefariousness was a threat that extended well beyond Star City, the ultimate demise of Malcolm Merlyn leaves behind many scars, especially for Thea. Malcolm corrupted Thea in Arrow season 3, taking her away from Star City to train her in the methodology of the League of Assassins. Ultimately, this was all to use Thea as an unwitting weapon to murder Sara Lance (Caity Lotz). Thea never forgave Malcolm for the physical abuse and emotional manipulation he subjected her to. Yet Malcolm is the reason Thea developed the combat skills necessary to don a hood of her own as Speedy and join Team Arrow. As Thea was reminded in "Lian Yu," in his own way, Malcolm loved his daughter.
Though Legends of Tomorrow has established that any dead character in the Arrowverse can be plucked from the timeline to reappear, death tends to be permanent in the Arrowverse. (Sara Lance's resurrection is a rare exception.) Malcolm's demise, unfortunately, robs the Arrowverse of one of its most versatile villains and denies fans of the sly charm and wit John Barrowman brought to the role. Merlyn was perhaps the foremost villain fans loved to hate in the Arrowverse. His appearances always denoted major happenings, and whether he fought alongside or against Oliver Queen and the forces of justice, Merlyn was always fascinating to watch.
What Malcolm leaves behind are questions. Chief among them: How will Thea process the loss of her "real" father? Will this be the impetus for her to don the hood of Speedy and actively fight evil as part of Team Arrow once more? How will Oliver react to the final bow of his longtime enemy? What's more, Malcolm was one of the last parent characters on Arrow. The last parent standing is Quentin Lance (Paul Blackthorne), the father of the late Laurel (Katie Cassidy) and Sara. With Malcolm gone, both Oliver and Thea Queen are now truly orphans, alone in the world with no family except each other. Though Thea "owes" Malcolm for her aggressive combat skills, his presence was a blight on her life and her development as a well-rounded person. Thea is ultimately better off without Malcolm Merlyn in her life.
However, Malcolm was often a creative deus ex machina for Arrow. He was a character of seemingly unlimited resources, able to know key elements of the plot as required, and could appear and disappear from scenes at will. (He was known to the League of Assassins, after all, as Al Sa-Her - The Magician.) Like the potential abandonment of flashbacks in future episodes, no more Merlyn in Arrow season 6 means losing certain storytelling crutches the writers used. This will hopefully help force Arrow to refine the way they tell their stories for the better in the coming season.
With Malcolm gone, the Merlyn flame has now been fully snuffed from Earth 1. While his time has come, the end of Malcolm Merlyn leaves the Arrowverse with a little less magic. Whether that's ultimately a good or bad thing remains to be seen, but Malcolm Merlyn will most definitely be missed.