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This article contains campaign details that may be considered plot spoilers. If you haven't finished the campaign yet, please be wary!
As the Cybran Commander, Ivan Brackman, delivered the final blow to Gauge's ACU, his escape pod pops off unnoticed with his parting message that Ivan's story is over and a new adventure for Gauge has begun, ending the mission. Ivan Brackman, knowing the ecosynthesizer space platform is too powerful and important to fall into wrong hands, decided to self-destruct Shiva Prime and subsequently flying away in a Cybran air/space fighter, talking with Dr. Brackman, who remarks that he needs to debug Ivan's Proto-Brain code.
Shiva's existence has come to an end, and with it the mislead civil war. Ivan Brackman makes his speech at the Coalition halls, imploring the UEF, Illuminate, and Cybrans to come together as one once more. Meanwhile, in the aftermaths of the UEF and Illuminate perspectives of the War, Dominic Maddox returns home to his family, having a slight limp, while Thalia Kael has been arrested for her crimes, and Jaran died during the time Thalia was defending the gate - much to her burning sorrow.
Meanwhile, in a very small building in the middle of a desert behind a large sandy rock like wall, Dr. Brackman's brain is seen in his large biofluid container, facing Commander William Gauge. While this is happening, the Father of the Cybran Nation talks about the issues of the Proto-Brain implant and William Gauge discusses reasons as to why they shouldn't proceed. Gauge then talks to Brackman, promising that he will not fail him again.
Finally, little to anyone's, let alone Ivan's, suspicion, Brackman's brain and what seems to be an unidentified Seraphim brain are seen merging together, as William Gauge supervises the procedure. What does this bode for the future of the UEF, Cybrans and Aeon is uncertain.
But time will tell all...