Madara's debut appearance as Tobi is Naruto Shippuden Episode 32: Return of the Kazekage.
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Yes it is true that Obito Uchiha is tobi as shown in Manga Chapter 599
I'm not sure of when Naruto fights Tobi alone, but there is an episode in Shippuden in which he fights Tobi with a group of six or so shinobi whilst on a quest for Sasuke. This episode is number 134, called "Banquet Invitation".
Naruto Shippuden Episode 99: Raging-Tailed Beast.
he doesnt come back til shippuden like 280
Sasori hidan tobi nagato kisame kohnan zetsu itachi deidara kakuzu orochimaru (former)