Hi, I'm relatively new to D&D but might be trying to run my own campaign soon. I was trying to figure out if there might be any enemies, NPCs, or spells that would be able to grant control over character's bodies?

I am aware of the spell Dominate, but was looking for something where self-preservation wasn't important, or where they may be able to control multiple people at once. How would this affect checks for deception since the character being acted upon wouldn't know they are lying?

If this is something that would need to be homebrewed, how might you work that sort of mechanic?

I’m hoping the idea is this is for a BBEG or bad guy generally. Don’t do it through magic, just make them charismatic. There are countless real world examples of people who can convince others to go and risk their lives or do all sorts of questionable things because they believe in and are loyal to the charismatic person. 

So not a direct answer to the question but as someone with a few years behind the screen, I'd like to ask why you really want this spell or monster?

Taking away player agency is a very very very dicey thing to do.  Even a spell like "hold person" is a tough one because it effectively tells a player "all you get to do on your turn is roll a die to see if you can do anything".  The more you force a player's character to do things the player does not want, the greater the chance for a rift at the table.  And then there's the "once someone's been charmed, how do we trust anyone in the group again" change to the dynamic.  Some games can really devolve fast if the charcters don't trust each other and the players have had too many things done for them by magical charm.

Just a heads up on some possible issues that can come down the road.

To be clear, I don't intend for this character to be entirely bad, but to be treated that way and hunted by those who are now in power, after genocide wiping out their people. This character seeks revenge. The people who are now in power are tasking you to kill him under false pretenses, but his aim isn't to kill the players, and it's proven several times during the course of the game. When players try to stop him, he would rather use Forcecage to keep them separated.

So, are you looking for an imposter type, then. This person didn't do it but was framed. Is that it? And you want it to be someone else took over his body and did the things?

If that's it, rather than a full takeover you could go with something like a changeling who took the character's form, or a spell like Alter Self or Polymorph. Or, if you want them to have fully taken over the body, you could go with Magic Jar.

Also, a pet peeve. I should hope no one's aim is to kill any players. The characters, however, are a different story.

No, he takes over other character's bodies (usually NPCs, but maybe a player at some point). But I'm wanting there to be a restriction on what he can do. I don't want it to be unlimited, and I want him to be able to be tracked. I was thinking of putting a distance limit on it, too. Perhaps he can only do it so much each day but then is exhausted?

I'm thinking there will be undead battling the kingdom and the characters, but that he won't really fight them unless necessary. My goal is for the players to empathize with him and for there to be a moral dilemma on what way to take this. I'm planning for it to be kind of a horror scenario, though.

If you want grief to be a really on the nose theme you could have him use spirits to control people.  That would be using a  ghost like creature as the manifestation of this power. It would also be easy to make that part of the reason for his group being attacked they could be shunned for a cultural practice of necromancy like ancestor worship. 

As for mechanics, there is the issue of side lining players  when using  possession mechanics.  There are ways around that  for example the actual mechanics can use spells like crown of madness, dissonant whispers and compulsion that give limited control or you can give the possessed person something else to do like a battle in the mind.  Spells are relatively easily framed as the intervention of spirits manipulating things. 

Awesome, I'll look into those ideas and see if they will work!

Thanks, I'll look into Magic Jar as an option and get back to you!

Magic Jar or Dominate seen like the best to use for it, so far, but I think Magic Jar might be better. I might still modify it a little, but it seems the best answer so far.