Right. So under normal conditions with that spell, the victim will think the thing, then act on the thing, all the while believing it did so totally on it's own until the spell ends.
That part does get a little wonky for spirits, who do know they cannot for example attack their summoner - but the spell is very explicit in what happens when you succumb to it, so they will do it anyhow, but the GM might have to fudge the thinking of how the spirit reconciles being able to take an action it otherwise would think it can't.
A mundane example: A spellcaster uses control thoughts to make a scrawny dude think he totally flip that car over, and to proceed with that idea. Dude should know damn well there is no chance that can happen, but the game mechanic effect of that spell supercedes what he thinks he knows and forces him to go for it.
Edit: Further example. Normally, players get to decide what their characters think, and what their characters do. This spell also supercedes that. It pretty much breaks all the rules, both in game and 4th wall. Most mind control spells in most games do.