I like the story.
How I think it went, is Cortana starts destroying things to make everyone submit, in an act to simply stop wars. 76 spartan 4s were ordered to stand against Cortana, so she destroys the training facility. The UNSC was trying to fight back so she destroys Sydney. The brutes posed a threat as well, and she confronted Atriox asking him to choose a side. She destroys their homeworld. The Banished somehow knew that the Infinity had a copy of Cortana to lock her down, and ordered to attack it.
The Infinity arrives at zeta halo, and is immediately struck with a stasis beam from four Banished dreadnoughts, which disabled its weapons and engines, and was drawing energy from its shields to give power to their engines (halo wiki on stasis weapons for reference), rams the Infinity. Atriox boards the ship and steals the weapon.
Cortana was expecting Chief to come down to delete her with the weapon, but Atriox came instead. Atriox had already defeated the UNSC and Cortana was met with certain death, if the ring came under the Banished control, they could use it to kill more people than Cortana ever did. So in an act to stop war, or delay it at least, she deletes herself and destroys part of the ring. She also puts Atriox in a time lock, where on the inside no time passes, but on the outside time passes as normal.
Everyone thinks Atriox is dead now, so when the Chief wakes up in the pelican, the Banished find the Harbinger and let her free. At this same time, Atriox is freed from his time lock. The Harbinger was sending Atriox the location where the Endless were being held.
A theory I like says that the Endless are precursor descendent. During the Forerunner-Flood war, zeta halo went missing for a while. The primordial and Mendicant Bias were making a plan for when the Halos go off, they genetically engineered the Endless which are immune to Halos. When the halos fired the Endless were found on their homeworld doing nothing really. They being so advanced, but having no huge starships or megastructures means the theory has some depth to it. So, if a species exists that can survive halo, if they were infected by the flood, would render the halo array pointless. Imagine thousands of years of trying to find a solution to something, you come up with a desperate last resort to solve the problem, and then only after it is executed there is another problem which makes your original solution pointless. “I tried so hard and got so far but in the end it doesnt even matter”.