Having rescued the remaining Little Sisters from Apollo Square, the Fatebreakrs took the sub of the now deceased Pressure Washer to Point Prometheus, the birthplace of the Little Sister project. The Sub rose up into the Bathysphere Metro Terminal, the Fatebreakers ready to fight.
"Soon as we surface in Point Prometheus, get ready. I'm sure Fontaine knows we're coming." Ethox said.
"It's a good thing we managed to find more Lot 192 in Suchong's lab to make sure we have a big enough dose for Johnny." Michiru said.
"Yeah, we can't take any chances." Ultra noted.
As soon as the sub surfaced, they saw Fontaine outside with Johnny as the two of them threw fireballs at the sub, creating a wall of flames.
"Alright, alright. You chumps lookin' to slug it out? I'm game." Fontaine radioed. "But I hold the Ace up my sleeve with all the ADAM in this city, and I ain't shy about usin' either of 'em! And now, I'm jake to take all this power I got for a spin!"
Fontaine then used inhuman strength to pick up a large object and tossed it aside, before he and Johnny retreated.
"What is this you all wait for? Go and get that idiot!" Tenenbaum said as the sub's hatch opened.
"Let's go, after them!" DJ said as they chased after Fontaine and the mind-controlled Johnny.
The group followed the two through a glass tube as Fontaine tried to block their path with fire, and even closed the doors on them.
"The mugs are all right behind us! I don't wanna even see them walkin'!" they heard Fontaine yell as Security Bots activated, shooting through the glass to try and get them, but the group easily destroyed them and pressed on, into the main hall where Fontaine was seen ripping a pillar down.
"Hate to cut and run, gang, but I got a little transfusion appointment to get to! Johnny, would you kindly kill every single one of 'em, and toss their bodies out into the ocean?!" Fontaine ordered as he shot the door controls and retreated through a closing door.
"Schiseee! You let Fontaine get away!" Tenenbaum said.
"We'll worry about him later doc, this is our chance to save Johnny!" Ethox said.
Johnny stood in front of the group, eyes glazed over and robotic as the room was silent. He made the first move, pulling out the Chemical Thrower and launching Electric Gel, the stream covering the entire length of the room.
"Duck!" Visha yelled as the group dropped down to avoid the gel. "Looks like Fontaine managed to get Johnny's arsenal upgraded."
"I'd call that convenient if it wasn't pointed our way." Peach said.
Nemo concentrated, flinging a knife to cut the tube that connected the Chemical Thrower to the ammo, rendering it useless. Johnny switched to the Machine Gun, blanketing the room in gunfire.
The 203rd members blocked the bullets with their shields, allowing Tanya to take note of the situation. "We'll never get close to him as long as he keeps unloading on us. We need to force him into melee combat."
"I've got a better idea! Ultra! Have Xurkitree wrap him up!" DJ said.
"Right!" Ultra said, sending Xurkitree. "Xurkitree, Wrap please!"
The Ultra Beast complied, its tendrils unbothered by the gunfire as it wrapped Johnny up, the mind-controlled man struggling to escape.
"Alright, now's our chance!" Ethox said as he rushed up to the restrained Johnny and pulled out one of the doses of Lot 192. "Time to wake up, Johnny! You're not a slave - you're a man!"
The Nobody plunged the needle into Johnny's arm, causing the young man to groan as his whole body shuddered, his mind deleting and rewiring itself. After a few tense moments, Johnny's eyes started to regain their normal expression.
"Wh-Wha? Where… I remember Ryan's office, then…" Johnny mumbled.
"So, you changed Johnny's tune, huh?" Fontaine said over the radio. "No problem, I got others. Code Yellow."
Johnny stiffened up once more, his wrists shaking and a cold sweat forming, signs of a heart attack.
"He's initiated the kill command!" Vicktoriya said.
"Bring the other dose!" Tanya ordered Aqua, who immediately ran over with the other sample.
"By the power of the Goddess of Water, you are healed!" Aqua declared as she plunged the other needle into Johnny's left arm, causing the attack to subside. Johnny breathed heavily, catching his breath.
"Johnny, are you okay?" Legolia asked.
"I… I am now." Johnny panted as he was released by Xurkitree, shaking his head. "What happened?"
The group then got Johnny up to speed. They told him everything. How he was implanted with the "Would You Kindly?" and "Code Yellow" commands since birth, Andrew Ryan being his father and how he was killed by his hands, albeit by Ryan's orders…. And of course, the truth being Atlas was really Fontaine all along, using him for his own gains.
"Atlas… was Frank Fontaine?" Johnny asked.
"Yup. He's been the one pulling the strings this whole time. He set up that whole Submarine Bay explosion with a fake family so we'd be coerced into killing Ryan. Now he's got full control of Rapture with all the ADAM in the city at his disposal. But not for long." Mirror Match said. "We are going to pursue him and end this."
"Just as soon as we figure out how to open the door he disabled the controls too." Kazuma said.
"The only way to open the door Fontaine went through is to have a little one open it for you." Tenenbaum informed them.
"Well, then I guess it's your time to shine, Sally!" Ethox said.
"Okay!" Sally agreed. "Let's go get that bad man!"
Sally walked up to the doors, crawling through the small Little Sister entrance, allowing her to open the door from the other side.
"Time to go, everyone! The angels are cheering us on!" Sally said.
"Well, guess we better make sure we don't let them down." Johnny said. "C'mon, guys. Fontaine's going down."