Apollo enters the Element school, where the Elements train. The new recruits - Apollo, Jun Lee and Tsugumi Rosenmeier - then enter a training simulator, and Apollo ends up being partnered with Silvia. In the simulator, the two accidentally shares a kiss. Later on, the Shadow Angels appear yet again, and Silvia, Sirius and Raika heads out to attack them. However, Apollo accidentally winds up in Silvia's Vector, and now they need to co-operate to fight properly.

Apollo wants to search for Baron, and goes missing trying to look for the Vectors. This leads the Commander to initiate a special exercise for the other Elements: Find Apollo. What they doesn't know is that the exercise has a special meaning, which is to work together as a team. When Shadow Angels attack later on, Apollo, Silvia and Pierre manage to learn this lesson, and they beat the Mythological Beast which has appeared.

After a small accident, tension arise between Sirius and Apollo. Later on, a Mythological Beast attacks Memphis, and Sirius, Silvia and Sirius head out to counterattack. However, it sends out a bright light which causes each of them to experience short, painful flashbacks. When they then try to unificate, they end up trying to kill each other.

The elements' fight against Sirius is interrupted by the military, who despatches a new fighting machine modeled on Aquarion piloted by Glen, who recovered by having some of Futaba's feathers implanted on him. Sirius tries to convince Silvia to abandon the humans and join the Shadow Angels just like he did, but Apollo intervenes to dissuade her.