The Matrix Exploded

The UTOPIA Project is nearing its conclusion. Here is a recap of everything I have been too lazy to previously describe:

• Aizen was replaced by Duke Ballistic, a basic powerhouse.
• The PCs were taken off active duty during a damage control period, and other programs filled in for them.
• While dealing with one Count Maledict, the UDO replacements were ambushed by unknown metahumans, and the PCs were called in as backup. After a long and vicious fight, Maledict was subdued, but one of the metahumans, an invisible one, escaped. The PCs were restored to active duty.
• A few days later, the PCs are split up to deal with a city-wide wave of crises organized by the SEA. Equinox was ambushed and captured. The others tracked him to the SEA hideout, where they managed to steal a copy of the UTOPIA-Scan program they had been using to monitor the city and rescue Equinox (with the help of the invisible mutant, for reasons unknown to them).
• Equinox, however, had had everything revealed to him by the SEAgents, and their arguments had swayed him back to their side. He split with the party.
• The PCs returned to headquarters, where they shared the revelations of Equinox with their superior. Knowing that awareness of UTOPIA contradicted the whole reason the UDO had been created in the first place, he escorted the PCs to a chamber where they could have their memories reprogrammed. The PCs, understandably, ran like hell, and within minutes they had gone from government-run peacekeepers to wanted criminals. Proteus was sniped in the head during their escape but just barely survived.
• They escaped through the sewers and took refuge in Equinox's old house, where they ran into The Hidden again (the invisible one), who sensed that he might be able to recruit the PCs in the fight against UTOPIA. When they agreed, he promised to look into ways to get them out. The PCs went back to the sewers to hide until they heard back from him.
• In the days to come, the conflicts between the SEA and the UDO, fueled by the PCs flight and Equinox's defection, broke into an all-out war, ravaging Utopia City. At one point, the PCs got pulled into the center of a battle between a radiation-controlling SEAgent and a UDOperative with a literal Hyperspace Arsenal. They thoroughly crushed the Operative, at which point the Agent thanked them and took off. The PCs dragged Arsenal back into the sewers, where they shared the true nature of UTOPIA with him. Aware that, knowing this now, he could not return to base without suffering a wipe, Arsenal begrudgingly stayed with the PCs as they returned to Equinox's house to eat.
• Inside, The Hidden met them again, having discovered a way to bring the PCs into the real world. The method, however, required them to completely wipe out the minds of several metahumans, making The Hidden reluctant to even bring it up. Before they could resolve the moral pros and cons, the lot were discovered by a squad of SEAgents, led by none other than Equinox.
• The resulting battle leveled over two dozen residential blocks. Arsenal, forced to decide where his loyalties lay anew, sided with the PCs and was fried for his troubles. Sok and True Thomas were knocked out (although they escaped death) by an SEAgent's electric cannon, but ultimately every single Agent was killed, Equinox included. The session ended with The hidden remarking on the effect this would have on the continuing street war between the SEA and UDO and the PCs, obviously UDO no more, gave themselves a new team name: The Balance of Power.