Okay, for one reason or another Joe is not in the safe house when Keane's men attack. Maybe he was checking on Andy and Nile, maybe he needed some fresh air, too, and it's not as if Booker could tell him why he couldn't leave the house. However, Joe's not there, Nile and Andy are not there and when Keane's men attack they only get Nicky. They can't take Booker (for reasons) and so Nicky is completely alone in the van, he's alone in the plane, he's alone with Merrick and then he's alone in the lab where Kozak does all the things she needs only to him.

And Joe's not there for him as support, like in the movie, when it gets especially bad. And since Kozak only has him, it does get especially bad!!

Of course Joe's on the way with Andy, Nile and Booker to Copley, where Booker betrays them and all that... and then they bring him to the lab, too, where he sees Nicky and he's in a really bad shape...