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Bill tries to talk Joey out of becoming a state's witness, but as they talk, Joey collapses. Bill follows him to the hospital.
When Gregory House is ordered to treat Joey, Bill makes it very clear that he needs time to talk Joey out of becoming a state's witness, so that House should not rush him out of the hospital.
When Joey is diagnosed with hepatitis C and Chase tells him that he could only have gotten it from drug use or homosexual activity, Bill is insulted and strikes Chase. Chase backs down, saying he has no idea how Joey could have gotten sick.
Bill confronts House again, saying that if it got out that Joey had hepatitis C, his reputation would be ruined. House agrees to treat Joey secretly. Bill also helps out with Henry's Baby Brother by showing House how to convince the toddler to co-operate with treatment by making them think you're serious about hurting them.
When Joey starts to recover, Bill and Joey reward House with a classic Corvette.
However, Joey takes another turn for the worse. He has an unusually high estrogen level and the only explanation that House has is that he has deliberately taking estrogen supplements. This probably means Joey is gay. House explains to Bill that Joey is probably turning state's witness because it's the only way he can live a gay lifestyle. Bill is angry, but doesn't lash out, and agrees to treat Joey on the assumption that House is right.
When Joey recovers, Bill is still upset, but alibis by saying that Joey's herbal supplements were making him sick. He makes sure going into witness protection is what Joey really wants and agrees to let him go.