I'm not sure what you mean by thoughts that came "against your will". That means that you were fighting those thoughts and trying to stop them. Is that what you intended?

The most appropriate word in this sentence would be involuntarily if you want to express that the thoughts occurred against your will. Here’s why: Involuntarily: This means something happened without your control or against your will, which matches your intention in the sentence. Example: "Some random thoughts involuntarily popped up in my mind, and I could not sleep at all." Unconsciously: This means you were not aware of the thoughts or they happened without conscious awareness. This might not fit well in your case since you are aware of the thoughts keeping you awake. Automatically: This suggests the thoughts arose as a natural response or habit without deliberate effort, but it doesn’t necessarily imply a lack of control or that it was against your will. For your context, involuntarily is the best choice because it directly conveys the idea that the thoughts were not under your control. I hope this helps :)

“Inadvertently” would also be appropriate

Great question! For what you've described, I would personally choose 'involuntarily'. This means 'without will' or that you didn't choose - or volunteer - to have those thoughts. But 'automatically' also works too in this context (which almost means the same as 'involuntarily', but instead of YOU not choosing the thoughts, it means 'the thoughts happened by themselves TO you, with no direct human control'). 'Unconsciously' means more like 'you weren't aware of the thoughts'. Hope this helps! You asked a great question here, as these words as so similar and have such nuanced meanings.