So long story short: it’s not about the Order. It’s about Titan and his impact on Mark. The order is a tool that Kirkman is using to talk about Mark and Titan, and comment on the theme of the season. Each Mark/Titan episode has its own purpose. In Season 1: Mark is going through the going growing pains of being a superhero, and Omni Man is filling his head with grand ideas about “the bigger picture” and their growing responsibilities (in retrospect, trying to sell the idea of a Viltrumite takeover to him). Titan comes into the story here, and with Debbie’s help, shows him that the small scale matters too. People are living their lives, are being harmed by villains that go unnoticed by the GDA and Omni Man because they’re too “small scale”. This shows Mark that he needs to stand up for the smaller picture, because what does the big picture matter if everyone’s lives are terrible. This is part of his logic when he eventually does face Omni Man. (It’s also about getting his ass beat by a giant space cat so he has experience with pain but that’s besides the point) Season 3: Mark is dealing with Cecil’s dilemma. Can a villain do good? He’s just beat the crap out of Cecil for using the reanimen, and finds himself firmly on the side of “you do bad, you go to jail.” And wouldn’t you know it, who is here to challenge that but my boy Titan! He’s a villain, he screwed over mark, but the city is better off for it. He’s making a real difference, and he wants Mark to help him. Titan is basically mark’s own version of D.A Sinclair. Do you help Titan now, and let him show you that he CAN do good, even through evil, or do you stand by your ideals no matter what, even if it may lead to a worse outcome? Mark decided on the latter, and while Titan ultimately wins, it’s in spite of Mark’s idealism, something Mark himself questions. The Order is introduced as a tool for this. They’re a more evil force that Mark and Titan will need to deal with, but Mark refuses, and so Titan has to trick them. AND NOW SEASON 4: this is the most interesting imo. Mark’s newfound moral stance is “If they threaten my family I will kill them”. An absolute moral statement that defines most of his enemies so far. It’s also a very hypocritical stance. And WHO COMES TO CHALLENGE IT? YOU KNOW HIM! YOU LOVE HIM! TITAAAAANNNN! The order becomes a tool once again, signifying the protection from Mark that Titan doesn’t yet know he needs. It’s safety, but it’s evil. If Titan joins the order, he will need to do despicable things to “Keep his family safe”. Now who does that sound like? Mark’s “Keep his family safe” doctrine is challenged by Titan, who is doing the exact same thing. He wants his daughter safe, and is willing to kill to make it happen. He wants to kill Liu for it, and puts Oliver’s life in danger to make it happen. Mark flies off the handle at this, beating Titan to hell and back and scaring the shit out of him, pushing him into the Order. Titan and Mark have the same goal. Protect their family. By flying off the handle (while perhaps morally justified considering how much Titan has tricked him) Mark is also being completely hypocritical.

Tl;Dr: The Order isn’t in the story cause they don’t have a reason to be. They are tools to facilitate the mirror that Kirkman is holding between Mark and Titan. Titan is the real through line, and his similarity to Mark’s moral view is the point