When activated, Tornado becomes sort of ethreal, despite still being perfectly solid. His legs disappear and are replaced by a wispy bit of body, just barely touching the ground in a tip. This bit is surrounded in a small twister, which happens to catch small bits of data from the Net in it, to Tornado's dismay. Apparently, they hurt his appearance. His helmet comes over his head but doesn't cover his face, only the back and top of his head. His hands do not look ghostly, they are very much whole looking. In this form, he creates tornadoes to attack for him.
Edit: I'd like to add a plot point explaining why Zeo has a new Navi. Without ViralMan's helmet, he is found by the people he was stolen from, and thus goes into hiding, and is currently in Zeo's home computer. Zeo leaves most of his battle chips there in case ViralMan requires defense.