It takes them a minute to process that Scotty is pointing a phaser at them. If it were me, I'd probably notice a gun pointed my direction pretty quick, but it's a lot more commonplace for Kirk and company than for me, I think.
Sulu unlocks them, and McCoy realizes that Scotty and Sulu aren't blinking and surmises they're drugged. Spock says neither did Jackson before he collapsed, and first of all, is he really walking around counting how often people BLINK? Also, Jackson was there for, like 1/2 second before he collapsed, and wasn't he already dead?
So they try to jump Scotty and Sulu, but suddenly they're in another room, with this bald dude. "Stop!" He yells.