Idea of Dark Jessica came up after remember the Metroid Prime Series Dark Samus and her nickname is Echo like how Dark Crono called Zando

Who made the Dark Ones was by Crono and his Brothers Father who made Zando original as a "replacement" for Crono has he never listen or follow his way, as for Echo he made her just to hunt down Jessica because he felt Jessica took Crono from him even though that's not true and he wanted to replacement

How they were created they where made of DNA of the person but about 60% to 70% of there body uses Dark Matter or what Dragon's call Living Matter, because it was learn even though a strong power source and material it was somewhat alive to a point it was like Parasite but it giving to a someone in a rare form it was infected and corrupt the host leading to death. Where in the case of creating Dark Ones with the added DNA and being in large mass the Dark Matter is able to Create a being of there own to do what they want but one mind set is always clear they will do anything to complete there mission or the find and feed off more Dark Matter.
The most effective way to stopping Dark Ones is with High Powered Energy weapons or pure plasma to pure light which can cause them the most if not the greatest damage against them, another more effective but more dangerous way is to used what's called Light Matter or Virus Matter which can kill off Dark Matter but will also make Light Matter useless at the same time its has the ability to reanimated the fallen and the dead back to life.

"Its unclear how many Dark Ones he can make or what amount of Dark Matter he has, but there are only 2 and 2 good enough" -Crono