Warning: Mild spoilers ahead for Marvel's Civil War story-line and potentially for 'Captain America: Civil War'. Just remember that this is just a rumor/fan theory, and should not be taken as cinematic fact!
2016! The year of the movie! It is packed with many comic based movies, and about every other movie genre. And one of the most anticipated movies being released next year will be [Captain America: Civil War](tag:994409). The movie is being based off the 2006 Marvel storyline, which features a hero vs hero competition, instead of hero vs villain. With Captain America facing off against Iron Man, Civil War is known as one of the most controversial comic story-lines because of the split.
The story sees the two heroes fighting against each other over the registration act (look it up or read the comic if you want to know the rest of the story), which eventually leads to Iron Man's victory (or Cap's surrender) and Captain America's death. Even though Captain America doesn't die in the Civil War, he does die in the preceding comic, but Civil War has a major effect.
One major character that is missing from the story line is Thor.
Why isn't Thor in Civil War?
Thor: Ragnarok (the comic story line) can be found elsewhere, but a majority of the story involves characters death, such as Thor. But we will get to that. As you have seen in the MCU movies involving Thor and Loki, you constantly see them arguing and fighting. Well, it's the same in the comics. Eventually though, Thor gets tired of Loki's treachery, and literally rips off Loki's head. But, sadly it doesn't end there, Thor discoverers that Asgard is destined to fall and be reborn forever, he rips the tapestry of time, allowing the people of Asgard to be free from endlessly going around in circles. But by Thor doing this, it eventually leads him to die.
Thor, however, is not in Marvel's Civil War, Ragnarok is. He is a clone of Thor, created by Tony Stark (Iron Man), Hank Pym (Yellow Jacket), and Reed Richards (Mr. Fantastic).
They create him to replace the deceased Thor, and to take an advantage over the Secret Avengers. But, it all goes wrong when the clone kills Goliath. Because of this, many heroes take Cap's side (such as Spider-Man), which helps turn the favor of the battle to Captain America and friends. Eventually, Hercules destroys the clone, getting revenge for Goliath.
A majority of the cast for Captain America: Civil War has been announced, and Chris Hemsworth (Thor) is not one of them. There have been rumors that Thor will make an appearance, but it is not yet confirmed.
Here's my Theory!
Now let's get on to my theory on the matter, keep in mind that this is just a theory, and you (probably) shouldn't believe it.
Thor does make an appearance in the beginning of Captain America: Civil War. But he is tragically killed (for all we know) by a villain on a mission in the first couple of scenes.
This also could set up for the beginning of the actual Civil War. Let's say that after Thor's death (since he is such a major hero), one hero accidentally causes some sort of destruction, killing innocent peoples lives. The government is angry about the situation, causing some form of the registration act to take place. Cap and Iron Man take different sides on the matter, and so on (read the comic). But since Thor is now dead, Tony begins building Ragnarok as a substitution for the absence of the God of Thunder. Thor eventually turns out not to be dead (most likely in Thor: Ragnarok) and takes his rightful place as the one and only Thor (not without a few epic battle scenes though).
We know that Thor does die (not for long) in Thor: Ragnarok, not Civil War. But the MCU has changed details in the comic/movie transformation before, and they will do it again.
Do you agree with me?
Remember, this is simply just my opinion and a theory. Do not take it seriously, because it isn't serious. And if you agree, great. But, if you don't, it isn't the end of the world.