Daxter was able to get the Mane 6 into the Fortress, an area connected to the palace which proved to be where Jak was actually being held, rather easily. Ben, with his new Disguise power, was able to sneak in right through the front gates while in the guise of a KG trooper who had been given special clearance to patrol the area.
Once inside and past the obstacles, the pair found Jak...undergoing Dark Eco infusion. At the sight of it, Ben shivered, the memory of undergoing the same torturous experience coming to the fore of his mind from the image and sounds of the device itself, and the sound of Jak's screams.
Two other humans in armor stood over Jak as the machine shut down.
"Nothing! I was informed that this one might be different!" The larger one stated as he gestured to Jak.
The smaller, younger one, who just so happened to have been the one leading the troopers who captured Jak when he first arrived shrugged.
"He is surprisingly resistant to your experiments, Baron Praxis. I fear the Dark Warrior program has reached a dead end."
Baron Praxis growled angrily, grabbing Jak by the head. "You should at least be DEAD with all the Dark Eco I pumped into you! Either that or metamorphosized like your friend! Why haven't you done either?!"
"What now? Metalhead armies are pressing their attacks. Without a new weapon, my men cannot hold them off forever." Baron Praxis' comrade asked.
"I will not be remembered as the man who lost this city to those vile creatures! Move forward with the final plan!" Baron Praxis ordered before gesturing to Jak. "And finish off this...THING tonight."
"As you wish," the younger human confirmed his order before looming over Jak. "I'll be back later..."
After making sure they were gone, Ben snuck his way inside and dropped his disguise as Daxter and the Mane 6 came in.
"Ding, ding! Third floor!" Daxter said. "Body chains, roach food, torture devices."
"Jak, you okay?" Fluttershy asked worriedly.
"Come on, don't be dead! Not after we've been looking for you for two years!" Rainbow pleaded.
"PRAXIS!" Jak roared as his eyes snapped open.
"Shhhh! Right now, we gotta get you outta here!" Daxter shushed. "Ben, you gotta the security lock for the chair?"
"I don't think that'll be necessary..." Ben nervously said.
As if to prove Ben's point, Jak burst free of the manacles holding him to the machine, smashing it in the process. Dark Eco flared over his body. His skin turned grey, as did his hair. His hair grew out much longer in dreadlock-like spines, and his nails turned into black claws. His eyes turned into black pits, staring at the world around him in fury.
"That's new!" Daxter meeped.
"Jak! Calm down!" Ben said as Jak jumped to his feet and looked around like a predator searching for fresh prey. "You're gonna bring every guard in the whole place down on our heads!"
Jak readied his claws to attack but then his eyes softened when he seemed to recognize Ben, followed by looking around to see Daxter and the Mane 6 all looking concerned at him.
"Whoa, nelly..." Applejack whispered.
"Jak's got Dark Eco powers now too!" Pinkie squeaked.
"Guys...you're all...okay?" Jak stuttered out as he turned back to normal.
Twilight quickly ran up and hugged Jak, followed by the rest of the Mane 6 plus Daxter and Ben.
"Jeez, remind me never to piss you off!" The Ottsel said, smiling in relief. "Come on, tall, dark, and gruesome, we're outta here!"
Jak then noticed Ben's KG disguise and was confused but his brother just smiled and shed the disguise, revealing his own Dark Eco powers.
"Praxis messed us both up, buddy."
"You more than me, apparently." Jak chuckled, internally surprised the humor even came out.
"Good to see you're still you after all that, Jak," Daxter praised, climbing up to his friend's shoulder.
"Oh, I managed to procure you some new clothes to get out of those garish garbs." Rarity said as she manifested a bundle of clothes and levitated them over to Jak.
"Thanks, Rares."
Jak changed into the new clothes, a blue jacket, white pants, and black boots and gloves. He was under no illusions that things were 'back to normal'. He could feel the pain of everything he'd been through hovering just at the edge of his awareness, and the rage was bubbling endlessly beneath his mind, waiting to unleash the new 'Dark Jak' once more.
He was focusing hard, holding all that at bay, shielding himself with the camaraderie and jokes. He needed to keep it at bay for now...at least until they were out of the Fortress. Once they were safe...then he could try and face it. Still, he had Daxter, Ben, and the girls with him.
"All that's left is to find Samos and Keira." Twilight said. "Let's move it, everyone!"
As the group made their way out of the lab where Jak had been experimented on, a voice called out from a communications grille.
"Alert! Prison escape in progress!"
"Is that us?" Jak asked.
"Let's not stick around to find out," Ben suggested.
As they progressed, Jak discovered that his jump boots Keira made him had been taken. However, as a result of the experimentation, he found he could now jump a second time in the air without them.
"Lucky we still have our jump boots!" Pinkie said as she, Applejack, and Rarity were able to keep up. Twilight, Rainbow, and Fluttershy just flew.
As they continued outward, they encountered a few Crimson Guards blocking their path. Nobody hesitated to strike them down, though at this point Twilight focused on using her Eco Blade since it was less noisy and more precise.
"Awwww, wish I could use my Super Eco Party Cannon to blast a way out..." Pinkie bemoaned.
At one point, however, the group came under fire, and Jak got a firsthand look at Ben's own Dark Eco powers, morphing his Dark Eco biomass into a large shield to block the bullets before reflecting them all back at the shooters.
Finally, they managed to make their way outside. Daxter cheered as Jak breathed in the relatively fresh air.
"We've got some friends who have been letting us stay at their place for the past two years. They should be more than happy to welcome you, BBBFF." Twilight smiled.
"Yeah, lord knows you need to eat something and rest up, Jak," Daxter noted.
"Hello, strangers."
The group turned to see an old man approach, along with a small child who looked oddly familiar.
"My name is Kor. May I help you?"
Jak started to step forward angrily, the rage fed by the Dark Eco in his blood. Before he could get a word out, however, Ben placed a hand on his shoulder and forcibly yanked him back.
"Sorry about him, he's a little... high-strung right now." Twilight apologized.
Kor hummed in acknowledgment before hearing footsteps and turning to see a squad of Krimzon Guards approach.
"Talk about being in the wrong place at the wrong time. I'd move on if I were you."
As Kor and the little boy moved out of the way, the gang all got on guard.
"By order of His Eminence, the Grand Protector of Haven City, Baron Praxis, everyone in this section is hereby under arrest for suspicion of harboring underground-"
The Guard's words were cut off as Jak's fist slammed into his gut hard enough to break his armor. The other Guards moved in quickly, and backup moved in from elsewhere.
"Oh yeah!" Ben grinned as he activated his Dark Eco Claws. "I needed to rip some fascists apart today!"
"LET'S WASTE THE NAZIS!" Pinkie cheered as she finally broke out her Super Party Eco Cannon.
"Well, no time like the present," Applejack said as she twirled out her Scatter Gun. "Just like old times, ain't it?"
At one point, Dark Jak came out again, smashing the Guards to the ground and shrugging off weapon rounds. When the last of that Guard unit was gone, Jak reverted to normal.
"You okay, Jak?" Ben asked.
"N...not sure," Jak replied. "I...I'm not sure I can...control that...side of me."
"Then I'll just sit on your shoulder," Daxter offered. "If you ever get too out of control, I'll bite your ear."
Jak chuckled. "Thanks, Dax."
"And if that doesn't work, I'll give you The Stare." Fluttershy offered.
"Oh yeah, that'll definitely work," Jak smirked. "Not even the most savage animal can resist that."
"Very impressive. What you just did was very brave." Kor noted as he approached before gesturing to the child. "This child is important."
"This kid? He looks kinda...scruffy." Daxter said as he looked at the child.
Twilight rubbed her chin. She had a pretty good feeling she knew who this child was already. However, Pinkie was already at the kid's side, making sure not to make him too uncomfortable.
"Awwww, ain't you just the cutest ever! I'm Pinkie Pie and these are my friends; Twilight Sparkle, Fluttershy, Rainbow Dash, Applejack, Rarity, Jak, Daxter, and Ben!"
"Um...I'm Mar..."
"Thank you for your help, all of you. But I must get this boy to safety." Kor said as he ushered the child along.
"Looks like we need to head to the slums, near the city wall," Daxter explained. "Right after we get some food in Jak back at the brewery."
Jak was introduced to Hilda, her mother, and The Eds, who were more than happy to prep Jak a hot meal. However, Daxter couldn't help but notice Twilight's pondering face.
"What's eating ya, Twi?"
"I know where we are."
"Yeah, Haven City," Daxter drolled. "Not that that tells us anything-"
"We're in the past. Or, at least, Jak's past..."
Jak stopped eating as everyone stared at Twilight in confusion.
"What do you mean?"
"Because that boy...that's YOU, Jak."
After a time of staring, Daxter was finally able to find his voice.
"Umm, run that by us again?"
"That boy, Mar...that's you, Jak," Twilight said. "I could tell from his hair, mostly but there were a lot of other features that gave it away."
"You guys are from the future?!" Ed excitedly asked. "Do aliens visit us from beyond the world?!"
"Uhhh...no, but we do live in a nice beachside village," Rainbow said.
"Maybe this was what Samos was acting all cryptic about back in Sandover..." Ben theorized.
Twilight nodded. "He said that something was going to happen that he wasn't sure we were ready for. And that it was going to be bad, and to get as many good memories as we can before it happened."
"Wouldn't that mean Samos is from this time, too? Isn't that the only way he could know?" Daxter asked before gasping "Does that mean there's going to be TWO of him now, too?!"
"Probably. So now, in addition to finding Keira and Samos, we need to keep my younger self, and Samos, safe." Jak muttered.
"Well, you're in luck!" Hilda beamed as she stood up. "Because we have some friends who have been DYING to meet you guys for the past two years!"
After leaving the apartment, the gang hopped into some unattended parked air bikes. Jak wasn't sure how he instinctively knew how to handle the controls, but he wasn't about to question it. It didn't take them long to find the back alley Kor had mentioned, but they were confronted by two people hanging around there.
One was a blonde female with blue eyes wearing a form-fitting green jacket, blue shorts, an orange scarf, and brown boots. The other was male with brown hair, blue eyes, and wearing what looked like Krimson Guard armor stripped of all insignia and identifying traits. He also had blue tattoos over a good portion of his face.
"We're looking for a guy named Torn," Jak said as the two approached aggressively, glancing at the man. "Are you Torn?"
"Maybe this guy's a mute," Daxter suggested.
"New faces make me nervous," The man grated out, his voice dry and gravelly. "But Hilda has been telling us a lot about you guys. Nice to finally meet you."
"Glad to see I could put in a good word!" The fat girl proudly said.
The man smirked. "Ya know, picking the wrong side could be...unhealthy."
"For the other side," Rainbow boasted.
"We want to see the Shadow," Jak demanded.
The man chuckled. "Not likely. I need to know you folks aren't all talk."
"We can do that. What do you need smashed, ripped apart, or blown up?" Ben asked.
"Nothing that big, at least not yet. We aren't ready for that level of confrontation." The man said before looking up. "But if you steal the Baron's banner from off of the ruined tower, and bring it back..."
"Petty vandalism? Really?" Rarity asked skeptically.
"In one piece, to prove your skill," the man clarified.
"We'll be rooting for you guys!" Hilda smiled as she and the Eds stayed with the man and woman while Jak, Daxter, Ben, and the Mane 6 headed off.
The ruined tower in question was actually outside the city proper, though still within the area protected by the Eco Dome. As a result, the gang encountered no Metalheads as they made their way there. The area looked like it had once been part of the city until it had been allowed to collapse into ruins. They had to avoid some swampy areas, but other than that faced no real obstacles.
"This seems more like a test of courage than of skill," Jak commented as they began climbing the tower itself.
"Probably is. Still, we should be careful. These creatures have been mutated by Dark Eco." Twilight said.
"I've noticed. I absorb some every time I kill one of them, and I can feel it building up inside me." Jak replied.
"Probably what powers up your Dark Form," Daxter commented.
"I've been absorbing it as well," Ben noted. "Nothing much aside from feeling it boost my body's regeneration."
"Oooh, it's kinda like a video game!" Pinkie cooed. "Hilda let me play some of the games she has with her."
Eventually, the gang reached the top of the crumbling tower, and Jak seized the banner off of its flagpole. As he did, the platform collapsed under them. Ben grabbed hold of Jak alongside Daxter as they fell, the Mane 6 doing the same with each other, only to bounce off a fabric awning, grind down a rope, and land right in front of where the man was waiting for them along with Hilda and the Eds.
"Yeah..." The man noted. "I guess you guys are in."
"Told you they were the real deal, Torn!" Eddy preened as he climbed up and rested on Torn's shoulder with a smirk.
Yup, Hilda and The Eds were part of the Underground from the start, I did imply that a few chapters ago, after all. It makes sense they'd let Daxter, Ben, and the Mane 6 know while they were staying with them.