I think it was to get Itachi to join the Akatsuki. I think that was their deal. In exchange for helping him destory the Uchiha, Iachi would have to join his group.
Like Madara, he didn't really care much for any clan including his own after the death of Rin. And as we saw in Shadow of the ANBU, Though filler, appearently he had been spying on the village for quite some time so he was aware of the political affairs that were going on at present. At least that is my hypothasis I could be wrong in this.
Nah it cant be... The first time he tried to destroy konoha Itachi was 4-5 years old. Also the reason why Itachi even asked for his help was because Danzo et had already asigned him the massacre mission and then Itachi stumbled across Obito spying on the village,so because Itachi's overriding goal was to protect the leaf he teamed up with obito because they had one mutual interest in exterminating the Uchiha. Itachi actually used that to his advantage to bargain for the leaf and sasukes safety so he killed two birds with one stone because he knew if the man he thought was Madara attacked the war konoha wanted to avoid would come anyway then Sasuke and his beloved village would probably die out.
Itachi chose to join Akatsuki as a spy for Hiruzen. He just put his balls to the wall in asking for assistance in slaughtering his clan to prevent the coup. In some mysterious twist of fate, they ended up helping eachother.
OT: Obito lost his way in the most undignifying way by anime standards.
I'm not sure I follow what you guys are trying to point out.
@ AshuraIsNaruto: True Obito did try to destroy the Hidden Leaf when Itachi was like 4 or 5. But the Uchiha massacre happened when Itachi was older. Yes Danzo tasked Itachi with the destruction of the Uchiha, but Obito had been watching the village even after his tussle with Minato. More in particular Kakashi. So he was well aware of Itachi's potential.
The Question you asked was why did Obito help Itachi destory his own clan right? Well didn't Obito offer his propsal before the massacre and didn't Itachi not give him an answer right away? Didn't Itachi then visit the 3rd shortly before the massacre? He ask the 3rd to watch over Sasuke. I assume during this conversation he informed Hiruzen of Obito's proposal.
Itachi chosing to enter the Akatsuki as a double agent happened after his conversation with Obito. I think that's how it went down if I am remembering the sequential events accurately. Obito wanted Itachi to join Akatsuki and in return he would help him slaughter their clan.
Itachi and Hiruzen used the opportunity to gather intel on the Akatsuki.
@ Andy Bogard: As stated above. I think Itachi chose to be a double agent after the proposal was made and he had informed Hiruzen. Then the night of the Uchiha Massacre aggreed to Obito's terms. I could be getting things completely wrong here. I would have to watch it again. I really don't pay too much attention to fillers XD
.