May contain traces of spoilers.
As I completed the main quest, there were quite a few things that didn't really make sense to me.
Why did Solas give the orb to Corypheus? He must have known it was a mistake, Solas isn't stupid.
Why did Corypheus sacrifice the Divine? There was no actual reason to go after her.
Why did the Divine think the Inquisition would change anything? If she had declared it after the Conclave failed, then it would have been a powerless organisation without a cause to rally behind.
Why were the Left and Right Hand of the Divine not with her at the Conclave? Weren't they supposed to protect her?
Why does no one blink when Solas insists that the Mark needs to grow stronger to seal the breach?
Why does no one tell the Inquisitor that they are being used and are merely a figurehead?
... and quite a lot more.
Well. With a few changes to the story we can close most, if not all, plot holes and answer those questions.
With hardened fronts on every side a diplomatic resolution of the mage/templar conflict was highly unlikely. They didn't even have enough trust to send their leaders. The Divine knew that for peace to return there had to be a common enemy and there was none available. That is, unless she created one. She had reached the end of her life anyway (perhaps was deathly ill and didn't have long left to live), so she ordered Leliana and Cassandra to rig the lyrium beneath the Temple of Sacred Ashes to explode. Her death and the death of all the mages and templars would allow the creation of a new Inquisition to find those responsible, with volunteers to join its ranks. It would be the opportunity to restore the Circles, the Templar Order and the Chantry.
Of course, something went wrong. The explosion was much bigger than anticipated and ripped a hole into the Fade. Ripples from the breach spread across the Fade, stirring up old things long forgotten. The Inquisitor is the biggest surprise though. While almost all people at the temple perished instantly in the explosion, they were at the right distance to be thrown into the Fade before the shockwave from the explosion could kill them. There's still a spirit helping them to get out and it does so by bestowing the Mark on the PC. Partial possession perhaps? Memories of an elven artifact made real through the incredible amount of magic energy from the explosion? A combination of those factors in proximity of the rift? Anyway, the PC falls out of the Fade and is being captured.
Leliana and Cassandra still deal with an unknown situation and make things up as they go. The difference is that they know full well who's behind the explosion. More importantly, now they have an even better cause and even a shiny new figurehead. Solas joins them because he recognizes that this power is something he needs for his own plans and Varric is the same as always. Josephine and Cullen are brought in because of their expertise and the Inquisition is starting.
The mission is to close all the rifts with the help of the Mark, which will give it more power until it becomes possible to close the Breach itself. That's the main reason the Inquisitor has to visit every last area in Ferelden and Orlais. It also explains why the mage/templar conflict doesn't seem quite as important. Once you ally with one side, the other one will attack Haven and cause an avalanche to bury it. You have to flee and Solas leads you to Skyhold.
After a while you notice that you aren't in power. Your advisors didn't even ask you before making you leader, they are responsible for the "Herald of Andraste" story and they lead the Inquisition in your name. You don't get much of an input, they keep you busy with picking out decorations, judging goat throwers and pseudo meetings at the war table. By the time you notice that you never get to meet any dignitaries or visiting nobles, that you aren't in command of your growing army and that you have no idea what your spies are up to, it's almost too late. Varric is the one who points it out to you, his animosity for Cassandra finally overrides his common sense.
You and most of your companions have to flee before Leliana has you removed. Vivienne sides with the Inquistion for more power. The Inquisition becomes your enemy, they now blame you for the explosion and put a bounty on your head. Luckily you have Varric's, Sera's and Iron Bull's connections. Blackwall and Cole can't contribute much but every little bit of help is welcome. Solas still pushes you to close the remaining rifts.
What about Corypheus, you ask? Well, he died during DA2:Legacy. Weak villain. Him surviving always made Hawke and Varric look bad. And let's be honest, Leliana is much more scary than he could ever be. Cassandra had some doubts at first but now she's too far in to turn back. They do what needs to be done, bloody hands and guilty consiences be damned.
What about the Grey Wardens? Well, they side with the Inquistion of course. The Breach is just as dangerous as the Blight and their treaties help to get more support.
What about Empress Celene? Well, perhaps you sneak into Halamshiral to sabotage a treaty between the Inquistion and Orlais. Maybe that's also a good opportunity to tell everyone the truth and perhaps gain the support of at least one side of the civil war.
Betrayal lurks close throughout the game. If you displease Varric or Sera, they will abandon you. Iron Bull is a mercenary and a spy for the Qun. He's not actually on your side, he just sticks around until someone makes him a better offer. Blackwall is a liar anyway, Cole is unreliable and Solas... hah.
It's you vs. the world. The organisation you helped build, the people you recruited... they are now your worst enemy. All the time you fight them Solas is waiting for your Mark to become powerful enough, then he'll use it for his own purposes, even if it means stabbing you in the back.
Your private war against the Inquistion can't be won by defeating their soldiers and agents in the field. No, you need to take out their leaders. Solas helps you by showing you a hidden passage that allows you to sneak into Skyhold through the dungeons. An epic battle ensues, pitting you against all your recruited agents, Cullen with his soldiers and finally, Leliana, Cassandra, Vivienne as boss battle. I'm fairly sure that would be a lot more difficult than Corypheus. Josephine can be reasoned with, if you don't kill her, too. Once the threat of the Inquisition is gone, you can close the Breach itself, bringing your Mark to full power.
Once the world is safe again, Solas uses the opportunity to betray you. He uses (blood) magic to control your remaining companions and knocks you out. You wake up tied to a ritual circle designed to transfer the Mark from you to Solas. He succeeds but both of you are throw into the Fade once more. You manage to get away and run into Flemeth, who tells you that Solas plans to use the Mark to unlock a special Eluvian and free the elven gods. She redirects you to her daughter, who should be able to help. You stumble out of Morrigan's Eluvian and somehow manage to convince her. Together you make your way to the temple of Mythal, to gain the knowledge necessary to find Solas and stop him.
One of you takes the power of the Well of Sorrows, fly to Solas on a tamed/transformed dragon and interrupt his plans. During the multi-phase battle Solas exhausts the power of the Mark and flees defeated, once more unable to unlock the Eluvian. You win! Post credit scene is the same, with Solas taking Flemeth's power. Cue sequel.
Leliana would make such a good villain and Cassandra is an excellent second in command. It would make for a much better story if you could show their grey morality, their descent, their justifications for all the wrongs they do. A hardened Leliana is not above kidnapping, assassinations, blackmail, torture and maiming... and she's considered one of the good guys. Take it a step further and you get a scary antagonist.
It's not necessary to pit more and more demons against the Inquisitor. Red Templars, mutations... that's not so scary. A world where you have to hide your identity, where you can't stay in any one place too long, where everyone hates you and wants your bounty... well... that's a dark and gritty story.
^^





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