During his debut we notice one thing - Tobi is not a member of Akatsuki. Rather he acts more like a subordinate than anything, staying by Zetsu and helping him as he can. We don't know much about what he did during this time, but we can assume he was helping by doing small missions for them and doing any tests required for him to be the first considered as a new member of Akatsuki. Sasori stated that during his fight with Chiyo and Sakura, he didn't have that hard of a time since joining, and Deidara was pushed into joined by Itachi; we can assume that since he was willingly following Zetsu, he was constantly tested.

Since Sasori's death Tobi has replaced him and become a full member of Akatsuki, being the newest member after Hidan. He knew nothing of the true goal and participated int larger, more difficult missions. His last mission prior to revelations made in chapter 364, was to kill Uchiha Sasuke who had 'taken over' his mentor Orochimaru. Akatsuki made every effort to find and eliminate him due to his extensive knowledge of Akatsuki's plans and secrets, in addition to his betrayal so finding that Itachi's younger brother had killed him was upsetting, especially to Deidara who wanted to kill him.

It's in chapter 364 that we learn that it was Tobi all along who was pulling the strings to the organization and giving Pein all the orders. Now that his former collegues thought he had died in his battle with Sasuke, he could move about freely as the leader and give orders to the group. Whether being a presumable member of Akatsuki was his plan or not is still under the microscope, but no doubt will be revealed soon.