Clarity

Clarity is an A.I created by Dr. Armstrong and situated in the Megaraph computer. Her goal was to protect life on the Moon. However, she came to see that both Formies and GPAs alike were violating this mission, and she plans to eradicate them to succeed in her goal. Freom originally was going to assist in this goal, before realizing after his defeat in Spark the Electric Jester that Clarity wanted to kill all robots, too.

History
Sometime before the events of Spark the Electric Jester, Dr. Armstrong created Clarity, and placed her inside the Megaraph computer, along with its function of mass-producing GPAs. He then created Unit-1 to protect the computer.

After some time or unknown event, Clarity reasoned that the only way to truly succeed in her mission was to kill all Formies. She compelled Unit-1 to assist her. The newly dubbed Freom then created a rebellion and transformed the main spire of Megaraph into a rocket to crash into the orbital ring.

Spark, however, tore his way through Freom's army, and eventually the rocket and Freom himself. From this defeat, Freom learned that Clarity was also planning to kill all robots, and rebelled against her.

Presumably, between the first and second games, Clarity created Astra to help assist in her goal.

Clarity reached out to Fark in Technoria City, begging the jester to help save the world. Before Fark can reply, though, E.J dashes through the sky, snapping Fark out of it.

Fark makes his way up to the Apocalypse Thruster, killing Astra in the process. Fark then destroys the Thruster and Freom, leaving only Clarity as a threat. Flint references this, saying that there is another threat to tend to.

Trivia

 * Clarity's name by definition means "the quality of transparency or purity". This alludes to her lack of a physical form, and contradicts her lack of purity, which is stated by Freom.