Here is my theory, after an hour of thought.
After Obito was crushed, he was found by Uchiha Madara. Madara realized that he was getting old, so he took Obito in, and trained him. Madara had to fake the death of Obito, to awaken Kakashi to become the 3rd mangekyou sharingan user required to awaken Tengu. However he knew that in order to summon Tengu, those 3 summoners needed to sacrifice themselves. So he needed to think of a way to not be involved in the sacrifice. So he thought of having not only Itachi and Kakashi be a part of it, but Sasuke as well. He saw that Itachi was special, and was capable of handling the job. So he assumed that his younger brother, who was just born, acquired the traits as well. He told Obito about the secret of the Uchiha clan, and the Tengu. Madara then told Obito that he could fix his right eye, and grant him more power than ever. Obito willingly accepted his offer, thinking that with the new power, he could protect the ones he cares about. What Obito didn't know, is that Madara was going to take over. Madara gave Obito his sharingan, which contains the blood of Tengu. His sharingan is at a level above Mangekyou. Tobi created Akatsuki and recruited an old friend, Pein. He needed someone he could rely on. His plan was to send Pein to kill the Uchiha clan, and take Itachi. He also said to spare Itachi's family, because their deaths would be inevitable. Tobi knew that Itachi would realize that he was not capable of beating Pain. He also predicted that Itachi would ask Pain to spare his family. He knew that Itachi would purposely wait for Sasuke to return home, before killing his parents. Both Tobi and Itachi wanted Sasuke to be stronger. Tobi wanted his strength to unseal Tengu, and Itachi wanted his strength to avenge his clan, and kill Pein.
Pein is the first member of Akatsuki. Tobi needed the perfect assassin to run the Akatsuki while he was away, and also be strong enough to do what he needed to get done. Pein is also the one who murdered the Uchiha clan. Tobi told Pein to kill every member of Uchiha, but spare only Itachi and force him to join Akatsuki. What Tobi didn't tell Pein, is he wanted Itachi for the sole purpose of using him to bring the other sharingan users closer to unsealing the great Tengu. Itachi tried to use his Mangekyou sharingan on Pain, but it did not work. Pein replied that his bloodline limit is the perfect counter to an Uchiha. Pein explained how his eyes can block any doujutsu. Itachi pleaded that he let himself be the one to kill his parents. Itachi didn't want another person murdering his family. Pein didn't think it mattered because he remembered what Tobi said, so he allowed it, and went back.
**Pein dies in a 2 on 1 battle with Naruto and Sasuke.**
Jiraiya dies the the battle against Pein. He saw that he wasn't strong enough to defeat Pein. Jiraiya knew that his death would spark a hidden strength inside Naruto, and that he was the one destined to be victorious. Jiraiya then dies smiling with one of his dirty books in his hand. When Naruto finds out, he obtains a hatred for Pein, and goes after him.
Kakashi dies in the battle against Tobi, after saving Maito Gai from a finishing blow. Before Kakashi dies, he looks at Tobi and remembers Obito risking his life to save him. Then he remembers his father risking his life to save his team, and how it was meant to be.
Itachi dies in the battle against Sasuke. Itachi found out about Tobi's plan, and he realized that if he died, his plan would be ruined. So Itachi purposely doesn't avoid Sasuke's finishing blow. Before he dies, Itachi tells Sasuke about the truth behind the Uchiha clan. Sasuke finds out that Itachi really did love him and his family, and that it was all set up to trick him. Itachi's eyes then turn white, as not only referring to blindness, but it is also symbolism of Itachi being pure hearted. Sasuke then falls into despair, holding his dead brother whom he killed, remembering how much he loved him. This sparks black hatred for Pain, and Sasuke's new mission is to redeem his brother's death, and kill him.