when did tony get the plague or something like that..

It was episode 22 of season 2!

Yes, I don't remember the exact episode, but it was that Tony opened a letter from a woman and as he opened it, powder was released from the envelope and the next scene shows the team being cleaned up and stuff. And later the blood tests show that everyone was negative except for Tony, he had the plague. But as you know he got better! ;). I guess it was around season 1 or 2 since Kate was still there! ;)

season 2episode 22 SWAK he actually has numonic plague and almost dies but he doesnt cause it has an antibacterial string that cant be fixed but it has a suicide chain so he doesnt

I bebelive it was anthrax that was released when he opened the letter.