He doesn't. Tony does, however, contract the pneumonic plague in the 23rd episode of season two.
Tony was almost killed by bubonic plague from a biological attack on NCIS.
No he does not die he recovers from being infected from the numonic plague. This is the episode before kate todd gets shot by ari. Also when Tony's beloved car gets blown up it is a set up created by jeans father who is the arms dealer tony has been following.
Season 2 - SWAK Season 5- Bury your Dead
Season 1 Episode 20 - Missing
Tony opens a letter that's sealed with a kiss and releases a powder into the ncis office. Then tony breathed in the powder and was infected with the plague. This plague has been gentically altered to not be affected by anti-biodicts. as tony is in iscolation kate tries to stay by his side during this ordeal, tony about to die gibbs rushes in and tells tony that he will not die, then he hits tony on the head and says did you hear me you will not die
SWAK, and its Pneumonic Plague, not Bubonic.
In the episode called 'Driven' (4x11)
He said~You are not alone.
They aren't dating