Rufus Shinra of the Shinra Corporation secretly helped AVALANCHE fight against Sephiroth.
Most of this theory comes from Final Fantasy VII: Advent Children, and how he appears to have been different . Fans assume this was his true nature all along; his goal to save the planet merely overlapped with AVALANCHE.
Unlike many things that Final Fantasy VII: Advent Children retcon, Rufus’ personality was not one of them:
That’s right. I’ll let you hear my new appointment speech….Old man tried to control the world with money. It seems to have been working. The population thought that Shinra would protect them. Work at Shinra, get your pay. If a terrorist attack, the Shinra army will help you. It looks perfect on the outside. But, I do things differently. I’ll control the world with fear. It takes too much to do it like my old man. A little fear will control the minds of the common people. There’s no reason to waste money on them.
In fact, his main concern was keeping Shinra in operation. For most of the game, Rufus was bent on power at all cost:
Rufus seems to have no love for his father, and schemes to overthrow him on the seat of power. He is initially portrayed as an enigma. Like his father, Rufus’s main goals are to control the world through the Shinra Company and increase the company’s power. Unlike his father, however, Rufus uses fear to control people, playing on their suspicions of AVALANCHE and Sephiroth to manipulate them.
AVALANCHE execution was to ironically quiet the fears of the public.
Rufus wants to have the two publicly executed to help calm the panic from the looming Meteor. His plans are foiled when Sapphire Weapon attacks Junon and blasts a hole in the gas chamber, Tifa, and Barret escaping on the Highwind that has been stolen by AVALANCHE.
AVALANCHE was able to escape because of dumb luck, not because Rufus secretly favored them.
His appearance On the Way to a Smile: Case of Shinra shows his evolution from cold and calculating to remorseful. It wasn’t only until he himself was negatively affected by the planet he exploited that he decided to change his ways.
In Final Fantasy VII: Advent Children, Rufus invites Cloud to see him. Rufus has been under the Turks’ protection for the previous two years, living with them in the Healen Lodge. He appears wheelchair-bound and is covered by a white sheet to supposedly hide his Geostigma, as he appears to be in the disease’s final stages. Renouncing his past cruelty, Rufus explains the near-death experience opened his eyes to the truth and he now desires to undo the chaos his company brought into the world. However, Cloud is unwilling to help Rufus.
But if this theory sounds familiar, it’s that it projects Reeves Tuesti’s entire character arc on Rufus.
Unlike many of the Shinra executives, Reeve shows sincere concern for Midgar citizens, and eventually, the Planet itself. This sense of empathy is reflected in what little is shown about his family; he is close to his parents. Reeve hates Scarlet, most likely because of her ruthless and inhumane personality. Tifa speculated Reeve stayed in Shinra and tolerating their inhumane nature because it gave him enough power to do some good by reducing some of the damage caused by Shinra.
Yet there is some truth to this theory. Rufus may be World Regenesis Organization’s main benefactor. The World Regenesis Organization is a volunteer organization whose primary objective is to help restore and protect the Planet. It’s head: Reeve Tuesti.