The Tunguska Iteration is an unknown substance that activates the Nanosuit's Spore Combating Protocols to a maximum. It is introduced via syringe and is given to Alcatraz by Hargreave at the end of "Masks Off" as a last hope of defeating the Ceph seeing as how he was unable to get the Nanosuit 2.0 for himself.
As stated above the substance boosts the Nanosuit's Spore combat capabilities to 100%. As shown in intermission cutscenes the Nanosuit at first simply trapped the Spore cells long enough to make them harmfull for Ceph. Yet they broke free later and continued their purpose. After taking the Tunguska Iteration the Spore cells are weaponized against unaffected cells - and all the Ceph - and start infecting them. This enabled Alcatraz and the Nanosuit to be able to process the large amount of Spore in the Central Park Hive and destroy all Ceph in Manhattan.