Reginald's (Colm Feore) trajectory was altered because he met and interacted with the Hargreeves siblings in Dallas, Texas in 1963 last season.
Disappointed by how the Umbrella Academy turned out, he purposely adopted a different selection of children and named them the Sparrow Academy.
By the season three finale, it became clear that this Reginald was as corrupt as the one that the Umbrella Academy was raised by.
He manipulated Klaus (Robert Sheehan) so he could win back the trust of the Umbrellas and Sparrows. He also killed Luther (Tom Hopper) using his alien claw in the penultimate episode, as a way to rally the remaining people.
This was all part of his plan to carry out Project Oblivion.
Reginald convinced the Umbrellas and Sparrows to walk through a portal that he built Hotel Obsidian around, which he claimed would have the solution to saving the universe from the Kugeliblitz (German for "ball of lightning").
The portal led to Hotel Oblivion, which was a machine in another dimension. Reginald sacrificed the remaining characters minus Allison (Emmy Raver-Lampman), whom he made a side deal with.
He began draining them of the particles in their bodies that give them their superhuman abilities, in order to power the machine.
To stop Reginald from killing them, Allison killed him with a scythe, revealing his alien head. Then she pressed a mysterious button that reset the universe.
In the new timeline, Reginald appeared to be one of the most powerful people, as indicated by skyscrapers with the Hargreeves name on them.
Reginald didn't get to complete his reprogramming of the universe, but he did get his wife Abigail back, who was previously revealed to be dead.
In the new timeline, the remaining Umbrellas and Sparrows are powerless and the injuries they sustained in Hotel Oblivion have been healed.
It's unclear if removing their powers was an intentional change that Reginald enacted in his reprogramming.