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Jill had found out she was pregnant, even though she had been using contraception. She also realized she had gotten pregnant at about the time she slept with another man because she and Charlie were having trouble. She was uncertain whether she should have an abortion and House didn't help by suggesting she have if her boyfriend looked like her husband.
Jill brought Charlie to the clinic on the pretext she had mononucleosis and he had to be tested for it. She cornered House who realized what was going on - she wanted to do a paternity test, House played along and eventually told Jill that Charlie was the father.