It’s heavily implied that the code red patient JD gets is the elderly gentleman from earlier in the episode - I believe JD, Turk and Elliott are all at the prescription window and JD suddenly says “that’s a code red” and runs off like he would any other episode, while Turk and Elliott continue their conversation.

After that, Brendan Fraser is exclusively seen with Dr. Cox, teasing him with patients and making him laugh with his colleagues, but he doesn’t have his camera (I’ll take pictures until the day I die) and nobody else can see him/can’t understand Dr Cox’s reaction to mostly serious questions/input on the job - only thing is that he is pissed at JD and refuses to leave the hospital then so “nobody else dies on his watch”.

The whole second half of the episode is this scenario, and it all culminates to Dr. Cox walking with Ben to, what we (and apparently Dr. Cox) think is jack’s birthday party. Cox says something to Ben asking why he doesn’t have his camera to take pictures of crying babies and shit, which JD then appears in a black suit asking Cox “where do you think we are?”.

That snaps Cox and the audience back into reality where we are at Ben’s funeral and he was a figment of Perry’s imagination the whole time, the code red was Ben’s cardiac arrest and Dr. Cox can’t process it because it’s his best friend.