Dr. Cox answers burning questions about ''Scrubs''

Last season, ”Scrubs” fans were left in a state of shock (get the defibrillator, stat) when Jordan (guest star Christa Miller) revealed Sacred Heart Hospital’s dark and dirty secrets to an unsuspecting staff. But the high-blood-pressure high jinks are just beginning. John C. McGinley, who plays J.D.’s intimidating mentor Dr. Cox, spoke with EW.com about what we can expect from the second season (debuts Sept. 26 at 8:30 p.m.) — including why J.D. (Zach Braff) could be shopping for baby booties, and the scoop on the cast’s very own fear factor.

What surprises await us in season 2?
Christa Miller, who’s married to our executive producer Billy Lawrence, is pregnant in real life. So Billy’s going to milk that. And considering that J.D. had a Mrs. Robinson with her last year, and Cox has courtesy sex with her all the time…

Do you know if Cox is the father?
I don’t know whose kid it is yet. I think they’re going to introduce a third character who’s shagging Jordan too. I’m guessing the kid isn’t mine, although I wish it was. It would be great to see Cox with a kid. But I don’t think we’re going to take the edges off that much.

How does the cast feel about following in the doomed footsteps of ”Inside Schwartz” and ”The Single Guy” as the follow-up to ”Friends”?
[NBC entertainment president] Jeff Zucker told us people are going to switch channels and watch the second half of ”Survivor,” that’s just the way it is. You’re going to lose 20 percent to 30 percent of your audience. But that still leaves 17 or 18 million viewers. The difference between us and those other shows is that they were unmitigated crap. And ”Scrubs” isn’t.

What’s ahead for Elliot (Sarah Chalke) this season?
In one episode, she tells me she wants to be treated as a colleague, an equal. So I give her the job of telling someone her husband’s dying. And when she comes back all sunny and chipper, she becomes the Angel of Death for the hospital for a little while, dispensing bad news for all the doctors.

It’s been said that some of the characters in the series are vastly different from when they were originally conceived. What’s been changed?
In the pilot, Elliot was written as this horrible bitch, and Sarah was incredibly miscast for that because she doesn’t have a bitch bone in her body. But instead of doing what’s in vogue right now, which is recasting and reshooting, Billy rewrote her as a ”Butterflies Are Free” Goldie Hawn with foot-in-mouth disease, which she’s fantastic at.

What about Dr. Cox?
I said at the first audition that he was way too similar to the head of the hospital, and that I didn’t want to play another prickly acerbic guy from hell. I wanted windows of redemption. And to Billy’s eternal credit, he worked with me. I mean, I certainly didn’t have any sense of entitlement to the role, because I had to audition for it four or five times.