The infrastructure of a galactic empire is not easy to plan, build, or maintain. Or at least it isn't for a mortal mind. Sio is far from mortal. She is not even a computer. The best way to describe herself so that a mortal can understand is a living intelligence. It took her newly a million years in time, as mortals understand it, to truly understand herself. She is Genesis's intelligence given life and a form of her own. Literally piece of her creator's mind was made real. He broke off a piece of himself and made her, but not in his image. He let her become her own being. He gave her the freedom to go her own way after he felt she was ready. Offered her a blank canvas to make her own, but she has never left his side. Not because she doesn't have her own ideas but because he is her father and her creator, and her love for him is eternal.
The foundation of any nation, kingdom, world, or star-spanning empire is its communication. The Imperium of Man was never able to master that simple concept. It expanded and expanded and expanded until the distances between stars became so vast that entire worlds were simply lost or forgotten in silence. Its chosen method of communication, which were astropaths shouting messages into the warp and hoping someone heard them, is so retarded that Sio could not even begin to understand it. All of this is because those in control believe that technology is either evil or treat its creation and maintenance as a religion.
Sio refuses to harp on this stupidity and sets about connecting her father's New Imperium. She does this by creating a modified version of the Phalanx and leaving it in each star system they visit. She called these info fortresses. On each world liberated by the enemies of mankind or the stupidity of mankind, she sets up an Infosphere as a part of the revival of each world. These Infospheres allow the people to communicate with each other as well as those on other worlds with them. All of these Infospheres are connected via the info fortresses in their star systems. These fortresses are connected as well, allowing for information and communication to flow freely through the Imperium. She uses this to freely transmit videos of what is happening on world after world, brought into the fold of the New Imperium, and help with the transition process.
The transition process, which on many worlds means the destruction of the current government and law enforcement bodies, is done either by asking them to stand down peacefully or by sending in teams to eliminate them completely. Most of the time, it is the latter.
Genesis's stance on the Ecclesiarchy is unwavering, and they are just eliminated period, and their massive churches repurposed. This can lead to the rise of two factions: those fanatics who fight to defend their religion and those who have already been marked as heretics for not believing it. They have both tried to create civil unrest, which so often led to world wars in the old Imperium. In the new, both groups are publically and immediately wiped out.
Sio is more effective and, at the same time, fairer than the Inquisition ever was. She can be infinitely brutal or eternally merciful, but neither comes without cause. She is not a machine. She is the Machine. She splits and leaves a piece of herself on every world they visit. That piece acts as the governess of that world. Each new world starts with a force of Cybers to act as law enforcement, medical personnel, soldiers, and more. The members of the Infinitum act as her staff on each world, helping to convert their brothers and sisters who still follow the teachings and beliefs of the Cult Mechanicum. They also do their work using their internal creation and uncreation engines to put new machines in place and remove the old.
If Genesis wanted to, he could do all of this himself, but he trusts her to oversee and manage his vision for humanity. Everything from revamping the health and housing system to instant terraforming. Sio does all of this and still only barely uses half of her immense processing power. She still doesn't see why her father doesn't just wipe the slate and start over, but his will is her command. His will is that humanity has a second chance. So, she intends to give them all they need, not to fuck it up again.