On their first mission in Andromeda the squad discovers an ancient ruin filled with technology left behind by the Remnant. While everyone is distracted, Lt. Harper suddendly shoots the krogan in the back and aims his gun at the rest.
"No one make a move!"
"Harper, are you mad?! What are you doing?"
Harper squints at you, "Mad? No, on the contrary. I see it very clearly. Our future. Humanity's future!... with this technology here we can become the dominant species in this galaxy!"
"Why? Why would you want that?"
Harper laughs sharply, "Because it's my legacy! I am destined to lead humanity to its apex!"
"What legacy are you talking about?"
"Cerberus, of course!", Harper smirks as he walks through the chamber, his pistol pointed steadily on you. "Many thought it died with my father, but ideas do not die. It will rise from the ashes like a phoenix, stronger and better than before!"
He picks up a glowing sphere from a nearby table and holds it to his eye, trying to figure out what it is. "With technology like this, we will be unstoppable! So... are you with me?"
"You are insane..."
"Insane? Insane?! You just can not see the big picture, this is--- ", Harper stops as pain suddendly flares up in his chest, looking down he's shocked to see a large blade penetrating him from behind. As his legs start to buckle under him and blood runs into his lungs, he looks back over his shoulder at the large synthetic warrior robot that stepped from the shadows. Vision becoming a dark tunnel, the last he sees is the blade crackling to life with electricity.
The squad watches in horror as the dead, twitching body impaled on the long, gleaming blade is ripped apart as the blade splits into two and expands. The massive robot crushes the skull with an easy step forward before incinerating the remains with long bursts of superhot plasma. The last of Cerberus is no more, gone completely, forever, no resurrection possible. He won't return as a phoenix.
The robot deftly picks up the energy globe and places it back on the table before turning to the rest of the squad.
"Uh... we are not with him?"
Staring at the squad for long seconds the robot reaches a decision and turns around, stepping back into its shadowy alcove and powering down.
That would be the only scenario in which I would want to see Cerberus in ME:A. 