I'm planning on writing a story where the Mongols are used as inspiration for the antagonists of the story. This is mainly because the Mongols were one of the few that interested me in my study of AP World History, but that's besides the points. I'm mainly looking for books and films, but if you happen to know of any articles online that give a clear and accurate portrayal of them that would be very much appreciated.
Well, there's their own secret history, you can find a translation of it here: https://jigjids.files.wordpress.com/2011/05/the_secret_history_of_the_mongols_the_life_and_times_of_chinggis_khan1.pdf
It's basically Mongol's own account of Genghis Khan, this particular translation being made by someone who is a Mongol himself and understands their religious traditions a bit more than your average translator. You still need to keep a critical mindset, as this is a first hand account, and likely unreliable in several places.
For your purposes, this may be better than a strictly academic book, just seeing what they thought was noteworthy enough to write down can tell you a lot about culture.
It very much depends what your interested in particular but for preliminary reading I would suggest The Mongols by David Morgan which is a relatively short textbook style introduction to a lot of the key points about the Mongols. Jack Weatherford''s Genghis Khan and the Making of the Modern World provides a nice popular history style companion although there are some issues I'm happy to get into if you want. Considering the angle your going for I think the most relevant one is that Mongol use of gunpowder is pretty debatable. Finally for something a bit longer and more comprehensive Timothy May's The Mongol Conquests in World History provide another excellent general work.