Omega Supreme is damaged, but not defeated. This chapter is a single arena fight against him, where Omega remains in the middle, and the three decepticons circling around the arena. While there is cover, it can be destroyed by enemy fire. There should be ammo and energon on the ring.
In the first half of the fight, Omega Supreme has four exposed turrets, which need to be destroyed. When the turrets are destroyed, Omega will requisition a battery, and you will need to quickly reach the battery to place the dark energon. Omega will take the battery to recharge itself, and the dark energon placed on it will allow it to be directly attacked. The second and subsequent batteries will have an aerial autobot escort. To defeat Omega Supreme, around 3-4 batteries need to be corrupted, before he collapses for the first time.
Despite the attacks, Omega still gets back up for the second half of the fight. Omega Supreme will slightly change his attacks, but combat mostly remains similar. The only target is to destroy the chest armor protecting the internal shields. Once the chest armor is destroyed, the chapter's end cutscene will commence.