In my train of thought, I would assume that Cortana with a billion AIs, each with UNSC ship, nation, and other native knowledge, is unstoppable. I believe, worse than Ultron. Especially with Guardians on her side that "one can police a solar system". Which on Genesis, you see like over 10.
In speculation, Cortana can not be stopped. She just EMP an entire planet and ships rotating it, nearly the Infinity as well, just under 5 seconds.
Honestly, Cortana sounds like she is absolutely broken in the story right now. If they find a way to beat her, thats surprising.
How can she be stopped? Well this could be a list but I’ll take out the unlikely ones as well as brief each point I make so it’s easy to understand.
Firstly, Humanity knows that Cortana’s weakness is the Chief, they could use the Chief to draw her out to a vulnerable position then they A) Kill her or B) Use her as bait for the other AIs to stand down, then lock them all away like BB did to all the ONI AIs.
Secondly, the Infinity is a strong ship, we don’t know how well armored Guardians are so they could resort to taking down the Guardians with MACs eventually reducing Cortana’s Guardians to piles of scrap. This leads to the UNSC winning then somehow they deal with the AIs and Cortana themselves.
Another way they could do this is by putting Spartans on to the Guardians which allows them to get closer to Cortana and eventually infiltrating Cortana’s base or Guardian (depending on where she is positioned) taking the fight to her. This will lead to them capturing/killing her, cutting the head of the leader. This could be a similar case to the fall of the Covenant, with Cortana’s AIs being uncoordinated and therefore easier to defeat.
The last one I can think of is the flood return, in a galactic threat level. They have amassed a large army and so the Created, Humanity and Sanghelli and other species such as Brutes maybe, must team up in order to fight off the flood. However as Cortana has the logic plague she decides to side with the flood. Cortana’s AIs feel betrayed by her and side with Humanity and the other allied species leading to Cortana and the floods inevitable defeat, but this battle is long and tiring for each species, but they eventually form a galactic truce or something similar to that to remember that fight.
So those are my possible theories for Infinite and I did save the most realistic and best story I could come up with for last with some lore bits thrown in (the lore being Cortana infected with the logic plague) but I wonder what 343 does have planned for Infinite and I hope they knock it out of the park, whatever it may be.