Unfortunately, I'm just getting to writing this at the last minute, so there won't be much time for you all to soak this in before we find out what really happened, but here it goes...
My theory is that Agent Phil Coulson is actually a Skrull.
In my version of the story, S.H.I.E.L.D. is already well aware of the Skrulls. They've been making secret deals for years. The Skrulls are allowed to roam the Earth freely in exchange for providing services as shape-shifters. As shape-shifters, they can take on the appearance of anyone, including, let's say, a beloved, but deceased, agent. S.H.I.E.L.D. was desperate, so they asked a Skrull to fill in. Now that they had a guy inside the most powerful organization in the world, the Skrulls saw their chance. The Coulson decoy gave them information. Eventually, S.H.I.E.L.D. figured this out. But they couldn't simply kill off the new Coulson, so they wiped his mind (insert a Professor X cameo or maybe tie in Scarlet Witch). The Skrull now believes that he is actually Coulson, and obediently works for S.H.I.E.L.D.
But it was too late. The Skrulls had all the information they needed to infiltrate our planet. They began sending in their own troops (disguised as other villains) to take out heroes. S.H.I.E.L.D. grew even more and more desperate, and they kept calling in Skrull replacements to prevent worldwide panic. Eventually, a large part of the world's heroes are replaced by Skrulls.
This is where tomorrow's episode kicks in.
The mind-wipe can only last for so long. It wears off and Coulson remembers who he really is. He goes on a rampage, and escapes Centipede. He returns to S.H.I.E.L.D., in full Skrull form and confronts his team. They are unable to stop him, and he escapes to join his fellow Skrulls. The episode ends with a Nick Fury cameo, as he explains to the team his reasoning for allowing the Skrulls to secretly invade Earth.
For the next few episodes, the team is on their own. They struggle to cope with what they've learned, but still carry out missions.
Then, whenever it may be, comes the season finale. Skrull Coulson returns. He tells S.H.I.E.L.D. to prepare. Prepare for war. For the Secret Invasion has begun. The episode is all about the Skrulls coming out. We find out which heroes aren't who we think they are. We see widespread panic across the globe as the Skrulls begin their attack. The planet is in chaos.
In any following seasons, we get to see how S.H.I.E.L.D. handles the Secret Invasion and their mistakes. The team we know now is in charge of rounding up the remaining heroes (plenty of cameos to please us fans). We get to see some epic battles, but keeping this a S.H.I.E.L.D.-based show, we see more of the post-battle cleanup. The team goes around searching for clues about the Skrulls and their weaknesses and whatnot.
So there you have it. It would be a real surprise for fans and allow for the Marvel TV Universe to expand. Again, its a long shot, but it's something to think about in these last few hours before the big reveal.
What do you think? Drop a comment!