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Only after Gauge levels the entire city with nuclear weapons does Thalia realize her mistake in unwittingly aiding Gauge's plans to find what he calls 'Shiva Prime.' On top of that, the Cybran convoy was actually on a humanitarian mission and the prisoners she freed were actually Royal Guardian commanders. The siblings learns of Maddox's defense of New Cathedral from Gauge and accompany him in his attack on the Coalition center of Quantum Science and Technology, hoping to send a message to the Illuminate government.
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The second phase (dedicated to the Aeon Illuminate) follows Commander Thalia Kael as she fights for a group known as the Royal Guardians to 'restore the Illuminate to their former glory.' After ambushing a Cybran weapons convoy, securing technology from a decommissioned Aeon facility, and freeing a group of Aeon political prisoners, Thalia, along with technical assistance from her terminally ill brother Jaren, defends a geothermal power plant from UEF forces, meeting the mysterious Cybran, William Gauge, when they request assistance. Zoe Snyder, who provides him with advanced weapons, commenting that her doing so is 'good for business.' Maddox defeats Rogers' forces and destroys UEF command, but destroys the stealth system hiding a hidden portal in the process, unlocking the second phase of the campaign. After failing to stop UEF Commander Lynch from destroying New Cathedral with nuclear weapons before the population can be fully evacuated, Maddox decides to go on his own mission to eliminate Colonel Rogers. Maddox, replying that his wife is Illuminate and is inside New Cathedral, refuses and goes AWOL. After defending a strategic weapons facility and encountering a mysterious Cybran in the Weddell Straits, Rogers orders Maddox to destroy the Illuminate colony of New Cathedral. After repelling the attack, his commanding officer, Colonel Rogers, takes sole command of all UEF forces on the planet. After a botched training exercise and an incident in Coalition headquarters, Maddox fights off rogue Cybran units at a communications array. The first phase of the campaign (dedicated to the United Earth Federation, or UEF) follows Dominic Maddox, a UEF officer who is married to an Illuminate. The ultimate aim of the game is to destroy the opponents' ACUs. Experimental units can be produced from experimental gantries (buildings with the sole purpose of building experimental units) or built by engineers.
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The final result of this development is the unlocking of experimental units, which are large, research-unlocked units and buildings with significantly more power than other units and buildings. Research points can be spent on faction-specific tech trees to add bonuses, abilities and upgrades, and to unlock more-advanced units and buildings. Some buildings and units are more advanced than others and as players' bases and research levels expand, so does the quality of their units. Players may also build add-on structures, expanding the capabilities of existing factories. Players can also build land, air, and sea factories that produce land, air, and sea units, respectively. They build mass extractors and power generators, which produce mass and energy, along with research facilities that produce research points faster. In both the skirmish and multiplayer modes, players start out with an Armored Command Unit (ACU), which is a large, powerful, construction-capable unit, as their avatar on the battlefield.