Chrysalis found that, as the days ticked by, Ellie and Isaac seemed to be perfect for each other, just like she originally thought she and Wildfire were perfect for each other, and occasionally took some time off from her little store, which was easier when the store wasn't fully ready. When they weren't out dating, or trying to find low level jobs to keep themselves hidden, Ellie eventually asked Isaac about his past and what he was trying to bury, though while it was clear that Isaac was a little reluctant to speak of the past, and who he had lost, he had seen what happened to Chrysalis and opened up. Ellie listened to Isaac and helped him through his ordeal, of having to remember Nicole and the fact that she was gone, but she was surprised, and pleased at the same time, to find that he was strong enough to face his past and not let it rule his life. She knew that Chrysalis and her ordeals had helped Isaac face his own demons, she was positive of that, and it helped to strengthen their bonds, which pleased Chrysalis to no end.
At the same time, however, Ellie made it her mission to help Chrysalis overcome her own demons, what little of them remained anyway, and the spirit of Amaryllis came forward every time they did so, as speaking of the past, in Chrysalis' case, was extremely painful, even when they didn't discuss the old queen. The one thing that Chrysalis had been hoping for, when she eventually had her own child and was able to pass on the Hive to them when they matured, was that she was remembered as a caring queen that did everything in her power to support her Hove, but she was sure that they would actually remember her as a warmonger. She could only blame her mother for enforcing that lifestyle on her, and herself for accepting that fate so easily, but there was no changing the past, not unless she was willing to find a time spell that would let her go back and do something about Crudelis' vile torture... but that, in itself, was something she shelved and forgot about, since that would have untold consequences for the future that she didn't even want to think about.
Chrysalis found that, while she wasn't undergoing therapy with Ellie and Isaac, she did gain some customers for her little shop and sold some of the items that she had imported to the warehouse that was attached to her store, though some of those customers she noticed were Unitologists and she smiled at them to let them know she wasn't a threat. She had quickly discovered that by acting like Twilight Sparkle, back when she was a simple librarian and not a princess, she actually made herself less of a target in the eyes of the Unitologists and more a person they might try to covert, but thankfully a quick hypnosis spell, to make them forget their intentions to convert her, and a memory wipe spell of the time they were missing was enough to stop that from happening. They still came back every now and then, to actually buy something from her, but it was always the red candles that she knew they used in their ceremonies, but she said nothing as she took their credits and let them leave with what they had purchased.
In addition to spending some time at the shop she also spent a good portion of her time meditating, as Ellie said it would help calm her down, though that also gave Amaryllis an excuse to appear in Chrysalis' mindscape so they could freely practice honing Chrysalis' new powers without blowing up part of the moon in the process. The first thing that Amaryllis had her sister do was attempt to fight the creature, the very monster she had became when she battled her mother, and she instantly found that she wasn't up to the task. Amaryllis had been expecting this and planned for such an event happening, as she started teaching Chrysalis the more basic magical spells that she knew, and had forgotten since she was starting to favor her Pulse Rifle, before they moved onto the next level of spells that they had been taught when they were younger. When she completed a lesson Amaryllis insisted that Chrysalis use her training to defeat a group of changeling guards, in their natural forms, or a group of pony guards that used the same tactics, though she was required to use certain tactics to defeat certain opponents before they knocked her out.
The mental training, to remaster spells and powers that she had long forgotten about, was taxing all on it's own and that was before they got to the expert level spells that Amaryllis shared with her, gleamed from the private library their mother kept to herself. It appeared that Crudelis believed she should be the only changeling with power and kept those tomes to herself, but failed to keep them under lock and key, allowing Amaryllis to read them from time to time and she memorized a good portion of the spells inside the various tomes, which she now handed to Chrysalis. Some of the spells Chrysalis learned were ones that she had seen her mother use, more in combat again her generals, while others she was sure that Princess Twilight had in her own library, though there were a few that she didn't recognize that seemed great to have a working knowledge of. Of course when Amaryllis ran out of things to teach her, and that happened about half a year into their training, she had Chrysalis face the creature again, who still beat the stuffing out of her, but once more Amaryllis anticipated that happening and had Chrysalis practice with her new power, instead of fearing it.
Chrysalis had seen what she was able to do against her mother, one of the strongest changelings in existence, when she harnessed the power that had been coursing through her veins, and it was still there, waiting for her to call upon her real power, but it actually terrified her. She had become a monster, one hellbent on killing Crudelis by using any means necessary, and she was sure that she could have hurt Isaac along the way, had she not forced her mother into the air and kept her there for the majority of the fight. She understood that Amaryllis wanted her to come to terms with the power that she had unlocked, the very power that had made her seek out the crystal mirror in the first place, but doing so was harder than she anticipated and every time she challenged the creature it would beat her. Fortunately the creature stopped when she admitted defeat and backed off, letting Amaryllis tend to her again, but it only made Chrysalis worry that she couldn't stop the creature she had become.
Amaryllis continued to insist that she needed to defeat her fears and find harmony with her new power, something that was odd for a normal changeling to think about, but at the same time Chrysalis did her best to overcome her fear of her powers, even if said power manifested as a monster that always beat her.
While Chrysalis did that Isaac and Ellie, on the other hand, eventually decided that they couldn't actually wait for an adventure to come to them and started researching the Markers, in secret so EarthGov and the Unitologists didn't find them out, which, after some amount of time, lead to Ellie visiting Haven Prime, which was her old home apparently. There she was able to make contact with someone that might be able to help her, and both Isaac and Chrysalis as well, in their search for anything related to the Markers and their origins, as they all assumed that some species had created them for a very specific purpose. Ellie was focused on finding what she called the 'Marker Homeworld', the place where the Markers came from and, if they could find that, they might be able to turn all the Markers, both the Black ones and the Red ones, off. Chrysalis had no idea if that was even possible, but since Ellie believed in that mission both she and Isaac supported her as best they could, while at the same time obeying her wishes to stay out of sight until she had more concrete evidence of the planet she was searching for and any information regarding the Markers.
During her time on Haven Prime, which made her miss Isaac and vise versa, she encountered John and Damara Carver, as well as their friend Robert Norton, and discovered that Damara was actually being assigned to Planet Uxor, or more specifically to where one of the Markers was being kept, and she actually promised Ellie that she'd share whatever information she could get, when she had the time to do so.
The fact that there was actually a second replica Marker in existence, as Isaac knew there was one near their own apartment building, didn't sit well with either Isaac or Chrysalis, especially since the Unitologists that Chrysalis used her mind spells on tended to come back and tell her things about what the 'Circle' was planning. It was an unintended side effect of her trying to make them stop attempting to convert her, but while Ellie was busy gathering information she got some of her own, fabricating a new mind spell to replace the old one and a new form to be associated with it, as well as making sure that they stopped coming here when they had things to tell her. As such 'John Dee' was able to gleam information from the Unitologists and sent them back to work without them knowing that they had revealed anything to an outsider, but every time it happened Chrysalis realized that something terrible was coming. That was because this 'Circle' was gathering an impressive amount of resources, in both credits, weapons, and ships, that someone would think they were trying to take out the existing government or something similar.
The knowledge that the Circle was preparing for war caused Chrysalis to keep a close eye on what the Unitologists were doing, because having any information on their enemies would be beneficial in the future, but even then she didn't like what she found, as it only confirmed what the mind controlled Unitologists had told her. Isaac was still shocked that she managed to break into the minds of two members of the Church, even low ranking ones at that, but Chrysalis didn't really mind, as it gave her information on what their foes were doing and allowed them to plan accordingly. As such there was something that she told Isaac and Ellie, when they were next together, that was more for Ellie if she found something and needed to investigate it, only to need to call upon the two of them in the event that she found what she and the others were searching for. It was a specific code, one that Ellie could give to a trusted person, who would be required to come to Chrysalis' store and offer her a very specific item, one unknown to the patrons that came and bought things from her all the time... a specific item that would be a call to arms, essentially being Ellie's signal that she found the Marker Homeworld and that it was time for Isaac and Chrysalis to come join her, with the person baring the item being their transport.
Isaac and Ellie raised an eyebrow when Chrysalis suggested this plan to them, as they were more surprised by the item than the plan she had offered, since it was actually so important to her, but at the same time they understood why no one else would even consider it... and soon enough the two of them agreed with the entire plan, while at the same time knowing that, at some point in time, they would have to act on it.
As it turned out it took the Circle two years before they started any operations, giving Ellie, Isaac, and Damara Carver to continue their individual investigations on the Marker's, the signal they produced, and the potential location of the 'Marker Homeworld'. During that time Damara happened to stumble across some information regarding the Sovereign Colonies, and more specifically their experiments with the Markers, leading Ellie and Robert to assist her in her attempts to find the location of the source of the Markers. Unfortunately something started to happen when Damara found that information, as the army of Unitologists that Chrysalis had heard about, fully armed thanks to the weapons and ships that they had been gathering for a long time, had finally started it's assault on the locations that contained a Marker. At first it started in the outer reaches of the territories that humanity controlled, but Isaac and Chrysalis, who remained hidden on the moon while Ellie carefully worked her magic, were horrified when they learned that the Unitologists were successful in 'liberating' the Markers of the planets they had attacked.
Chrysalis used her natural ability and took the form of one of the Unitologists that had been sent to one of the locations they wanted to attack, where she noticed some postings that detailed the chaos and death that came when one of the Markers was activated... meaning not only were the Unitologists activating the dreadful Markers, but they were creating multiple Necromorph outbreaks.
Isaac wasn't shocked when he heard that news, as they already knew that the Unitologists were insane, and this only told him that the Circle was a group of extremists that appeared to be more armed and better trained than they originally assumed, because they were able to slaughter the soldiers of EarthGov in the areas they had 'liberated' the Markers from. At first Chrysalis thought that such a thing was strange, that the people that were employed and trained by EarthGov couldn't stand up to the extremists that were attacking them, but then she remembered that she had been bested by civilians and a couple that was in love. Despite that fact she watched the shadows and kept an eye out for danger, as it was only a matter of time until the Unitologists arrived on the moon and attacked the building that contained the Marker, as it was a definite target for the Circle. Fortunately Chrysalis had stored her Advanced Suit in a storage chest, along with her weapons, that only she could open, while Isaac kept his Plasma Cutter on hand, as his armor had been sold off to make him seem more like a civilian... something that she didn't agree with, considering the danger, but at the same time she didn't criticize him for his decisions.
Eventually bad news reached them that the Circle had attacked Uxor, which was where Ellie had done because it appeared that Damara had found something that was the breakthrough they were waiting for, though Ellie insisted on Isaac and Chrysalis staying hidden for now, so she could verify what Damara found. From what the duo was able to determine the site the Marker was being held in had been breached and another outbreak had occurred in the process, something that the two of them had been expecting when they heard the news. Uxor was joined by a number of other planets and colonies that had been attacked, revealing that the Unitologists were attacking the majority of the locations at the same time and that they were getting close to 'liberating' the remainder of the Markers. That knowledge told the duo that the moon was soon going to come under attack from the Circle and their forces, something that quickly became apparent when Chrysalis discovered something unpleasant when she was sneaking through the offices of the higher ups in the Church.
That something was a pair of text logs that seemed important, as the first one was about Ellie and stated that she might actually know the location of the Marker Homeworld, which was another reason why they attacked Uxor, and the second contained some notes on Isaac, revealing that the Unitologists knew that he lived somewhere in the New Lunar Horizons Colony. What she discovered was that there was an order out, to all the members of the Circle, to hunt down and exterminate Isaac if they found out where he lived or encountered him in the streets, along with capturing his friends and allies, if he had any, to force him out of hiding. That made Chrysalis happy that they had used one of her own personas for the apartment, that way it would take them longer to figure out where Isaac was located, while at the same time being somewhat pleased that neither Isaac or Ellie had any other friends or associates at the moment, because that meant that the Circle wouldn't have any leverage against him, provided they didn't capture Ellie at some point.
Despite the fact that erasing evidence of what the Circle knew was likely to point them to the New Lunar Horizons Colony, and make them think that Isaac was here, she went ahead and, using her limited knowledge of the technology that was inside the offices she had infiltrated, she purged all the data relating to Isaac, Ellie, and anything else that might help them find out where they were hiding. Once that was done she headed back to the apartment, making sure to use a different route than normal so she could see if anyone was following her, and she smiled as she lost the small group of people that had been following her, while at the same time wishing she could have struck against them. She was too close to the apartment building, so killing them would have drawn attention to this area, and using magic to strike them down would have raised questions, so she held herself back and slipped into the darkness... while at the same time using a small bit of her power to send the Unitologists that were following her on a wild goose chase to the more populated part of the colony, where they were going to remain for a few days until they figured out they had been tricked.
She knew she was much stronger than when she had been when they were on the Titan Station, if her power up and mental training with her sister were anything to go by, but even now she wondered what was keeping her from beating the monster that rested inside her mind, what sort of test she had to overcome to use her full power. Part of her didn't want to use that power, because it was so easy to become a real threat to those around her, but she was sure that, at some point in the future, she would be able to figure out what she needed to do. Until then she made sure that Isaac was kept safe, as he was the Marker Killer that the Unitologists were afraid of, and ensured that no one came looking for him that wasn't sent by Ellie, if she had survived the events of Uxor. Chrysalis was fairly sure that Ellie had survived, because she was a fighter and wouldn't go down without taking a lot of Necromorphs down with her, so she knew that they just had to be patient and wait for her signal to arrive, or for her to come back and get them herself.
As the days ticked by, however, both Chrysalis and Isaac saw an increase in Unitology blimps flying around the center of the New Lunar Horizons Colony, with the leader of the Circle, Jacob Danik, promoting his believes as the blimps flew over the area. Chrysalis knew what that meant, as she had seen the reports from what the other members of the Circle did on the other locations that housed the other Markers, and she knew that time was running out, so the moment they saw the blimps she had Isaac prepare himself. That meant locking the door to the apartment and only opening it for her, since she was the only one who knew where he was, and Isaac was quick to go with it as he started to worry about Ellie, which was understandable since they had heard nothing from her since she went to Uxor. At the same time Chrysalis returned to her shop and remained there or an extra hour every day, longer than what was necessary, in the hopes that Ellie or her trusted messenger would come through the door, looking for her and Isaac.
Eventually a day came where the Unitologists, all armed to the teeth, ran down the street outside her shop and continued towards the EarthGov building that was nearby, one of many that were required to get through if they wanted to reach the Marker... and yet she did nothing, because the code hadn't been used yet, and she sighed as her patrons fled for their lives, leaving her alone in the small building until someone came along. Fortunately she didn't have to wait very long, as about an hour later the door opened, and the bell rang, as two soldiers walked into her shop, and she could tell that they were soldiers by the fact that they were carrying guns and wore armor that rivaled her Advanced Suit. As Chrysalis watched them she noticed that the soldier that was the closest to her seemed to be the commander of their little group, as he walked like a military officer or commander would, while his partner seemed to be a soldier who cared more about following orders than anything else. Both of them had hair that had been cut short, much like what Isaac and other members of the military did, though while the first soldier's armor had blue patches on it the soldier behind him had red patches on his armor, though whatever that meant didn't matter to her in the slightest.
Since the two soldiers seemed to be looking at the shop, and weren't paying attention to her at all, she decided to act like the owner of the place and cleared her throat, letting them know that they were being watched and that she was eager for some business.
"Welcome to my humble shop," Chrysalis said, thankful that she was still wearing her librarian disguise and easily slipped back into her persona, where she wondered what Princess Twilight would think if she saw the former changeling queen acting like a human version of herself, complete with a near identical voice, "Is there anything I can help you with?"
"Yes, yes you can." the commander replied, turning towards the counter as he and his companion stopped in front of her, where Chrysalis carefully stared into their eyes, as she could tell that neither of them were going to play around and were going to get to the point as fast as possible, "A friend of ours, Ellie Langford, told us that you might be able to help us locate Isaac Clarke, the so called 'Marker Killer' that the Unitologists fear."
"Isaac Clarke?" Chrysalis asked, though she did so in a way that made it sound like she had no idea who the name belonged to, which was what she did whenever someone came asking for him without producing the necessary item that only Ellie could have told them about, "I'm sorry, but that name doesn't ring any bells. I'm sure that I can help you find a different Clarke, as I know several that might be able to help you out..."
"Look lady, we didn't travel all this way to play a game with you!" the commander snapped, where he reached for his weapon and put a hand on it, indicating that he was willing to shoot her if he needed to, while at the same time his companion seemed shocked by what he was doing, "We know that you know where Isaac Clarke is, so tell us where he is and we'll be out of your hair."
"I told you, I don't know who this 'Isaac Clarke' is." Chrysalis replied, though as she said that she prepared herself, because if the commander fired she would take him out before his bullets even reached her, and she had stored a good portion of her medical supplies from the Titan Station with her armor, "Please, there's no need for violence. I'm sure that there must be something else I can help you with."
"Captain, I've got this." the second soldier said, to which he pulled out a pack that he had been holding onto the entire time, one that was well hidden behind his back so that Chrysalis wouldn't see it, and set it on the counter, before pushing it towards her, "Ellie said that the key to finding Clarke was to offer this item to you... and hopefully she was telling the truth, otherwise we wasted time by coming here."
Chrysalis looked down at the package for a few seconds and carefully opened it, as she was sure that these were the people that Ellie had sent to recruit her and Isaac into finding the Marker Homeworld, or how to turn them all off, and she let a smile appear on her face as she looked down at the red amaryllis flower that was in front of her. Only Isaac and Ellie knew that her sister shared her name with the flower, especially since they were the only ones that knew Amaryllis was even there, but this was what she was waiting for. Anyone could have offered her such a flower and expect some reaction out of her, though the mention that this was the key to finding Isaac was the other half of the code, to which she sighed as she covered the package back up and set it aside... before she looked at the soldiers again.
"Okay, you've found me." Chrysalis said, this time surprising them when she spoke in her natural voice, though at the same time she pressed a button and sealed the door to the shop, before turning towards the one door behind her that only she had the key to, "And allow me to answer your question; yes, I do know where Isaac Clarke is."
"Why use this approach?" the soldier asked, while his commander just stared, as if he couldn't make sense of how she was able to change her voice, without something attached to her neck, "Why not give Ellie a encryption key, or something similar, that we have to hand over to you?"
"Mostly because I don't know the ins and outs of your technology," Chrysalis replied, though at the same time she stepped back and moved a cover to block them from seeing her, but she kept talking as she changed back to her original form and slipped back into her armor, "besides, only two people knew what the significance of the amaryllis flower was, to me anyway, and only one knew the exact wording that needed to be said when it was offered. If you hadn't offered me the flower or the code phrase... well, let's just say you both would be dead and I'd be waiting for someone else to arrive. The fact that Ellie told you two exactly what you needed to know, and you performed your part of the code almost perfectly, means that she wants us to come and join her."
"That's correct." the commander said, as he was now focused on the task at hand and wanted to get this over with, while at the same time Chrysalis sensed that there was something more in his tone, "Ellie thinks she's found the source of the Marker Signal and, since both you and Isaac destroyed two of them in the past, she felt that it was time to bring you two into the mix."
"Then what are we waiting for?" Chrysalis inquired, to which she pulled the cover back and stepped out, wearing her Advanced Suit and carrying not only her Pulse Rifle, but both of her bone blades as well, causing the two to stare at her as they realized that she wasn't a simple librarian or shopkeeper, rather she was a warrior equipped for war, "Follow me, I have a shortcut to where Isaac is staying... and please, do refrain from annoying him when we get there. He's been rather upset that I confined him to the apartment, for his own safety, and that we haven't heard anything from Ellie since she last visited us, so this should give him some good news."
"Well we had best hurry, because the Unitologists are approaching the concourse," the soldier said, to which both he and his commander followed after Chrysalis as she lead the way into the alley behind the shop, before heading off in the direction of the apartment building, "I'm John by the way. John Carver. And this is my commander, Robert Norton."
"It's nice to meet you two," Chrysalis replied, though at the same time she smiled, as these were the people that had been helping Ellie earlier, while she and Isaac were keeping themselves hidden, meaning that they understood the mission that they were undertaking, "My name, my real name, is Chrysalis. Now, let's go find Isaac and give him the news, and then leave this colony before the Unitologists come looking for all of us."
She was sure that their enemies would be looking for them, based on the information she had read in the past, but at the same time she drew one of her bone blades and prepared herself, because she knew that things were about to change and a whole new adventure was about to begin for her and her friend.