20 years after the events of FF7, Shinra has gotten somewhat back on its feet with the new and optimistic motto of rebuilding the world, though it only really meant Midgar considering the other cities were not quite so affected by Meteor as Midgar was.
After the defeat of Deepground, the WRO got back on track and continued relief efforts and the building of Edge. It was not until several years after that, that Shinra itself was made known after it had gained back some of its old strength. Employees that had remained loyal to Shinra even after all of the events surrounding Meteor, especially those who were in the know to not blame Shinra for Meteor itself started to filter back into their old positions in the company.
The Turks worked their hardest to secure and destroy dangerous projects left over from the Old Shinra, and the branch that had remained with Rufus gained more members over the years, scouted from unusual places.
One of the most prominent features of the New Shinra was the opening of a health facility for members of SOLDIER that had gained complications involving mako exposure and Jenova enhancements along with remaining victims inflicted with Geostigma. Aerith's spring was guarded from those willing to destroy it in order to make a profit selling the miracle cure for the stigma, with blessing from the former members of AVALANCHE (and they had no real choice because otherwise it would be a dick move after all that money Shinra had poured into the WRO and the health facility.)
Reeve continued running and operating the WRO until he grew too old to remain in the position and stepped down in favor of his second, Yuffie Kisaragi. Living in retirement, he wrote books about his adventures in Shinra and outed even more of the Secrets of Shinra, much to Rufus' constant chagrin. For some of the more ticklish aspects of Rufus' past, he sent some of the Turks over to have a talk with Reeve.
As for the Turks, after Tseng's death (although, unbeknownst to Rufus it was actually a cover up in order for Tseng to join the secondary branch of Turks which had defected previous to the events of FF7) Reno assumed the leadership of the Turks. His approach to the Turks was, needless to say, considerably different than his predecessor's.
Wutai, in the aftermath of Shinra's downfall, regained some of its former power and prestige mostly due to Yuffie's influence and the importation of goods from Wutai in order to help rebuild the Midgar area communities.
Junon, as one of the last remaining intact bases of Shinra, became the default headquarters in the later years for Shinra's new efforts in righting the past mistakes the former incarnation of the company had done. There had been some resistance to Shinra retaking the property belong to it, but little was done about it due to Junon's own government and court system ruling that Shinra had proven ownership satisfactorily, and as they were continuing humanitarian efforts saw no need to confiscate the resources. Besides, nobody knew the codes to get into the warehouses except for upper Shinra personnel and lock down had been triggered by an emergency signal coming from the Midgar Network just before Meteor.