The Phantoms are an enigmatic group appearing not long after SRF made their way into the stars. They make their first appearance attacking the SRF-003 Calnus as it heads towards Roak. Later it is learned that the Phantoms are in fact created by the Missing Procedure using information gathered by the Grigori and energy obtained though them. These forces begin mercilessly attacking inhabited planets and other ships than their own, and will not stop until they are destroyed.
Near the end of the game, the Phantoms have expanded to Eldarian and Cardianon copies, including native animals and monsters from the galaxy. From what little intelligence gathered at En II, the Morphus have no idea of the mysterious group's identity, so they call them Phantoms, hence the title. The Phantom ships and crew give a crimson liquid-like appearance.
Phantoms are usually only encountered on Nox Obscurus. However, the first time encounter with them occurs on Aeos where the crew of the SRF-003 Calnus do battle with Phantoms that have taken form of SRF soldiers. In this battle, the Phantoms seem almost never-ending, as more and more ambushes occur, pushing the party to their wit's end. Though a Phantom force of this magnitude is never encountered again in battle (or of any enemy force), it serves to display their unending power.
When encountered in battle, Phantoms are incredibly stronger than what lifeforms they mimic. All but few Phantoms are resilient to dark elements while being weak to light elements.