I played the game and I'm getting the feeling that the anime will have this kind of ending...
Spoiler:
* There is also an additional "bad" ending exclusively for Phantom Integration that can be found in Chapter 3. In order to acquire this ending, you must have completely fulfilled Cal's path back in chapter 2 (choose to make love to her) and then choose to search for Ein in chapter 3. This will follow the "Road of the Cerulean Sky" ending until it reaches the duel between Reiji and Cal. Here, Reiji is unable to keep his promise to Elen and hesitates in shooting Cal, allowing her to win the duel. Cal stands there and wonders why Reiji didn't shoot. A moment later, she is interrupted by Scythe arriving in the church with the Zahlen Schwestern in tow.
* Scythe is pleasantly surprised at the outcome of the match and compliments Cal. However, she seems dissatisfied and impulsively betrays Scythe, causing a shootout between her and the Zahlen Schwestern. Time passes until nightfall and Cal is lying down wounded on a beach, presumably winning the battle at the church. Elen arrives at the scene a moment later, seeking revenge against Cal for killing Reiji. However, Cal makes no motion to defend herself and simply lies there, appearing regretful for the events that transpired. Elen in turn loses her motivation to carry out her vengeance and looks up sorrowfully at the night sky. Nothing they do now will bring Reiji back, and so both of them can do nothing more but lament their loss.
I wouldn't be surprised since from the anime I'v seen produced by BeeTrain, I get the feeling they always prefer a female-character ending or something like that.