My psyker got up to 12 levels of fatigue. Funny story about multiple perils of the warp, and critical damage ...

But after the 'pass out' option what's supposed to be the downside to the fatigue? and at what point do stims stop being effective way to wake someone up? I had him awake but pretty useless at 6 fatigue (TB of 3). If he could be stimed awake at 12 he could just use dull pain to be back to no fatigue in a minute, that doesnt seem like fatigue is that damaging then.

If you're racking up that much Fatigue, I'd rule that the character simply can't be roused, and is unconscious for several hours (enough to remove the Fatigue).

Personally more than double your TB I'd start making toughness roll to not go into a coma. Using a stim to bring bring some 12 fatigue down simply wouldn't maybe 3 stim, but then there would be toughness rolls see if your heart could take it.

After he rolled up 6 (double his TB) I wasnt letting him wake up anymore even with stims, but the heart attack stuff would be a good incentive to not use stims, I think I'll try that next time. Still I don't like the way a minute with a psyker with dull pain can still take that all away.

I'd rule that Stimm is normally sufficient to remove as many Fatigue as would normally render you unconscious... so a TB3 character dosed with Stimm would lose 4 levels (one more than his TB), and if that isn't enough, you need more. Of course, more than one dose in a day means you're subject to the rules for excessive drug use in the rulebook (every dose after the first within a 24 hour period requires a Toughness Test with a cumulative -20 penalty or the drug will not take effect)