The Basic order of events in OWP I'm using is this:
Optimus finds the Allspark and is reformatted.
Megatron boards the Orion looking for the Allspark and is instantly smitten with the pretty warframe.
Optimus is not smitten and kicks him out of the airlock even faster.
The ship crashes and everyone is in stasis.
Sari is born and the Decepticon generals discover where the Nemesis was last seen.
Sari stumbles aboard the Orion, receives the Key and wakes the crew.
The events of season 1 take place with some alterations.
Soundwave more or less joins Team Prime as Optimus’s son while still reporting back to Megatron. This is less about spying and more a custody agreement neither of his parents are aware of.
The Decepticons sense the flare ups whenever the Allspark brings something to life, but are otherwise unable to locate it.
Black Arachnia manages to piece things together and confront OP. While being unwillingly fused to the Allspark is different from becoming half organic, there are enough similarities to her situation for her to sympathize.
Starscream also figures it out, and while Shrieking that the era of Holy Primes is long dead, attempts to pry open Optimus’s chest plates. He doesn't succeed but does gain a fragment of metal from Optimus, infused with the Allspark's power.
Megatron is ressurected, Optimus finally figures out how to fly, and Starscream is killed only to be ressurected by the false fragment in his subspace.
Jazz, Ultra Magnus, Sentinel, and Blurr all come to visit.
Ultra Magnus (falsely) is told that Optimus died shortly after spontaneously reformatting as a warframe. They take a sample of his coding back to Cybertron, and Blurr is left behind to secretly observe Team Prime.
Soundwave overhears Magnus and Perceptor discuss "modifications" that were performed on newly emerged sparks and relays this information to Optimus.
Optimus realizes that he was always meant to be a warframe and is greatly upset by the idea that his teammates were also robbed of their proper frames.
The Allspark reformats Team Prime.
the Jettwins are made, and it is revealed that Soundwave stowedaway on the Elite Guard ship. Optimus is very upset that his baby is so far away, the Allspark responds by creating more mechs.
Events of season 2 more or less happen
Blurr is rescued from Master Disaster and is reformatted. This affects his security codes and he loses contact with Cybertron
The Allspark has apparently decided that any modified Cybertronian will be reformatted regardless of how close they are to Optimus.
Sari gets her upgrade early, and while Black Arachnia doesn't lose her spider mods entirely, she does become more comfortable in her frame.
Starscream's false fragment slowly loses power the more he uses it
The Elite Guard make a return trip to Earth and gets reformatted. Optimus is forced to reveal to them that he is alive, but manages to hide the Matrix for now.
All of Optimus’s babies are under one roof, finally.
Ratchet blackmails Shockwave into protecting Optimus, but Shockwave still informs the Decepticons of the truth.
Having kept well informed of mythology by his hunt for the Allspark, Megatron realizes that Optimus is not a Prime but a Prime
Megatron chooses to earnestly Court Optimus
Optimus is still not very enthused
This is a very lore accurate to what I wanted to happen in this AU.