Big Surprise: You discover that the Remnant of Argon is actually the souls of a lost Argonian tribe (Root-Whisper Tribe) that had originally placed their souls into the Remnant of Argon to save themselves from an evil alyeid necromancer trying to take their souls centuries ago. When you discover this you find out that Kassandra was actually using you all along. Kassandra was leading the Blackguards and you the entire time to try and find the Egg of Argon in an attempt to use its power to commune with the Hist. An ability she does not have, as she was born in Morrowind, outside of the Hist. Despite this may cause harm to the Hist and the souls trapped inside.

Final Part of Story: When you defeat the final boss, and rescue the Remnant of Argon you find the Hist is now awakening, and wishes to free the souls from the Argon, and itself, from its hibernating state. You must free the souls, and save the Hist tree, by entering inside the Remnant of Argon and selecting a companion to be a guide for the trapped souls. So the souls may one day return back into the world of the living. As Argonians usually reincarnate through the Hist when they die, but due to having to hide in the Remnant of Argon for so long, the process is no longer possible without assistance. Thus they need someone to help guide the trapped souls back to the Hist and in turn the living world eventually. While your other companion stays to become the new Root-Whisper Tribe leader. The Hist of the newly reborn village is suddenly flourishing once again and vibrant, while the new village now contains mixes of the other tribes you have already met in Murkmire, with the souls you saved one day will be reborn as the future children of the tribe.

Kassandra thought the Remnant of Argon could help her connect with the hist tree. I'm talking the real connection with the Hist, not the temporary communication that would break your brain if done for too long that you see the player doing occasionally in the game with the Hist. You have to understand that an argonian that cannot connect to the Hist is seen as... Defective, handicapped. They cannot understand many emotional ques of other argonians, their language jel requires a connection to the Hist to fully comprehend (someone can learn bits and pieces of the language but will never grasp it like a true argonians. As Jel is more then about speaking and is considered "a language closest to true thought". Though pidgin like communications have appeared from non argonians trying to learn jel, it is still not the full language.) She cannot partake in any of the more important traditions or rituals of her people. Even rebirth after death is impossible without the Hist. The Hist is a guide, way of life, literally connects them all, is the very language, minds, life and death of the argonian people. To be cut off, is to not be argonian.

Kassandra saw an opportunity to get something she desperately wanted when two different groups would go after the same object. All she had to do was point them both in the right direction and watch them run. Then simply side with whichever looked like would reach the Egg first. The Blackguards were most likely promised the relic after she was done with it, but were hopelessly disadvantaged as they needed to understand argonian culture and a way to commune with the Hist to find where the Remnant of Argon was even located. Something they were clueless on how to do. It wasn't like it was trapped in some random Xanmeer. The Cyrodilic Collections respected argonian culture, and had the aid of two argonians who with the help with their connection with the hist allowed them to find the Remnant of Argon. So all Kassandra had to do was make a move when she thought one group was getting close. She was just increasing her chances to win, that's all.

Kassandra did not trust that the Cyrodilic collections would stop her from using the Remant of Argon, as it as unknown if harm would come to the souls trapped inside, or the Hist protecting it, by using it in such a way, and the Collections were very sympathetic to argonians and their culture to probably risk it. While the Blackguards didn't care at all what happened to the argonians and probably just wanted the relic for profit. With the Blackguards, she could safely do whatever experiments with the Remant of Argon without anyone stopping her. So long as they were promised the spoils of the relic afterwards. Which is why Kassandra fled when she stole the one way the Collections found to discover the location of the relic, and sided immediately with the Blackguards afterwards, to protect her from the Collections trying to save the Remant of Argon from her.