Serious knee help

ok,I have been having issues with my right knee for three weeks. Last week the PT told me it was a fat pad issue. He loosens it and tells me to have at it. So I did about three four mile runs with almost no pain. Then I got a bike fit and my seat was raised by two inches. I don’t really wanna mention who did the fit, but it was someone who really knows there stuff. Today I did a duathlon and now my knee is swollen and bruised. Obviously I am icing and taking NSAIDs but I am not sure where this came from. The pain started about five hours after the race. The pain is way different from the pain a week ago. It hurts less when I straighten my knee and the bottom of my knee cap is really tender. So the question is what’s wrong with it?