I remember one episode from The X-Files (I think) where aliens contacted people.

They were using weird language and people were trying to decode it to understand what they want. I remember that they have their spaceship hidden in the ocean or something and in the final scenes, (I don't remember why) people decided to nuke them and when it was too late someone has decrypted their message which said that "they're coming in peace" (and then was the nuke explosion and probably end of the episode).

I don't really remember if it was The X-Files, or another sci-fi movie, but I remember the alien in the monitor was similar to the ones from The X-Files (big head with big eyes).