What was the meaning behind the Alejandro music video by Lady Gaga?

Well lets start off with this:

In the video she clues about Pro-gay movement, Anti-Nazi messages, and free mind expression. The Nazi's were to express the treatment that gay people go through. Many Gay people were burned alive by regular people. Just like the Nazi's did the Jewish. also if you watch when the guys were marching. The metal was a Jewish Star. Also when the boys were in the leather coats and doing the dance they had a badge on there right arm that was the Nazi's sign which had X mark through it.

One thing you may be confused about may be, "Who is Alejandro?":

Alejandro died because he was gay and was part of the military. She refers to the "Don't ask, Don't tell" law in the army. Once they found out he was gay they sexually abused him which led him to death. This happens in real life and she wanted to reach out to it.

Plus, Lady Gaga IS Alejandro in the video, she is telling the story of Alejandro in the video. At the beginning she is holding Alejandro's heart at his funeral. Than she goes into the explanation of his death.

Now to the "religious" aspect of the video:

Some people say she is showing Illuminati references in the video because of the upside-down cross. Well no she is actually questioning religion. When I say questioning I mean that she doesn't thing some aspects of it aren't right. As you know she is Pro-Gay and as a catholic to be Gay is a sin and SHE is gay. Which leads to the end scene where she burns in Hell. There is so much to it but it is really hard to understand if you don't watch her interviews. SO thats really all I can explain about the religious aspect.

Now on to the end:

She is praying for forgiveness because HE (Alejandro) is Gay (Remember she IS Alejandro in the video) and you can't take back some sins. Which at the end shows that she/he died.