The story might not be completely accurate but I will try my best.

the phoenix force is roaming threw the galaxy and and runs into cybertron and the surrounding stars systems. The phoenix sees the transformer civil war and isn’t happy about it. So it decides to go and destroy their home planet cybertron as a punishment for the war. when it gets to cybertron it is shocked to see that cybertron is really primus.(cybertron finished transforming before the phoenix arrived because optimus prime warned primus when he saw the phoenix).The battle begins when Phoenix starts attacking primus. The phoenix begins shooting powerful energy blasts at primus while primus starts shooting back with his powerful energy cannons. The battle goes on like this for a while until primus traps phoenix with an energy force field. It hold phoenix for a while but then breaks out. Seeing that at their current power levels it will eventually end in a stalemate. So the phoenix runs of to the nearest star and absorbs it’s power then returns to face primus.(the travel to the star and back took about 5 seconds) Phoenix releases a powerful blast destroying a lot of primus’s body. Primus quickly uses the omega lock and restores him self and gives himself a powerboost. The battle goes on again with phoenix and primus attacking each other and every time primus gets hit he uses the omega lock to heal himself and phoenix using energy from from future generations to heal itself. Phoenix decides to try to completely obliterate primus before he can use the omega lock so phoenix releases a super powerful blast that obliterates the omega lock and almost completely obliterates primus. Primus with whats left of his body uses a powerful blast to the extent of his strength on the phoenix that severely hurts it. Phoenix then absorbs more energy thus healing itself. Primus’s body then dies and his spiritual energy form is released. phoenix thinking it won prepares to leave but than is struck by a sword. It looks around and finds that having destroyed primus’s body it has released the more powerful spirit energy primus. The battles begins yet again but only for a while as phoenix is overpowered by primus. Primus than uses his sword and slices phoenix in half than decimates it by destroying it completely with a very powerful energy blast. Primus than restores every thing to what it was before the battle (except the phoenix).

After comments:
Phoenix’s psychic powers don’t work on primus because he has a processor. Phoenix can’t absorb primus when he is in spirit energy form because he is not really energy. primus is manifesting itself in a form of energy and whenever phoenix tries to absorb it he merely decapitates his energy form and reforms somewhere else not to far away (he does that in a millisecond)

tell me what you think of the story but no bad comments only helpful criticism. I wrote this based on what I know of both entities.