First off I would like to ask each and every one of you to respect each other and that you post NO spoilers, flames or inappropriate language (keep the 3,4, or 5 letter words to yourself, and you know what I mean by that) Thank you in advance for you consideration!
Now, onto the Theory!
We don't know much about the original timeline but here is a quick summation of what I believe happened. In an unaltered timeline many people went about their lives with no mysterious abductions or returns. A brilliant man by the name of Kevin Burkhoff was working on developing a method to unlock the unused portions of the brain when he fell irreversibly ill, some time after that another researcher came along and picked up where Kevin had left off. Through this person's research an amazing discovery was made, promicin. Also sometime farther in the future a catastrophe occurred that resulted in the deaths of hundreds, thousands maybe millions of people, this seems to have been of biological and industrial origin, and perhaps resulting in something much larger. After this catastrophe a select few are able to live comfortably within a "special city" created by an "elite group" while those less fortunate are left outside in a barren waste land struggling to survive. A group of people formed together, tired of the way things were and devised a plan.
There were members from both sides of that city who joined this group, they desired to see a better future and set forth to discover how to make this happen. With each other's cooperation they were able to get information, resources and technology to help them on their quest. They studied out their history and found key factors resulting in the origin of the catastrophe. They learned how it all began and what actions may help either prevent or significantly soften the blow of the catastrophe. They began a search through time to find people who, if at the right place, the right time with the right "stuff", were the best candidates to make the necessary impacts and decided on 4400 people who were removed from their own time. These people were brought to the future where they were given promicin, some of which seem to have possible suppressed memories of important information from the future and they are placed into a pretty glowing ball of light and sent back through time, Superman style, to Seattle in 2004. These people are brought to a secure facility and quarantined while they are tested and studied for a time and eventually released, unbeknownst to them, to begin their work. We learn that the future are responsible for the return of the 4400 when a young man by the name of Shawn Farrell heals his cousin Kyle Baldwin, who has been in a coma since Shawn's abduction. Kyle wakes being very confused and eventually leads his father, Tom, to a beach where they are able to contact the future and we are told where the 4400 had been and that they have been returned to prevent the catastrophe.
We see a few examples of the effects right off, one is with Orson Bailey who is upset when his previous employer refuses to give him his job back and he approaches the man's house and unintentionally causes his death. Later we see that this man was up to no good and that Orson may have done the world a favor. We see another man, Carl Morrissey who upon discovering his ability decides to use it to clean up a beloved park and unfortunately dies in the process. However thanks to his actions others in the community take action and continue his mission to clean up the park and perhaps more. Perhaps the most fascinating would be Tess Doener, a disturbed lady, who with her ability and a possible suppressed memory from the future created a device that brought the brilliant Dr. Burkhoff back to his senses! Dr Burkoff, the "Father of 4400 Technology" will become very important due to his knowledge and understanding of promicin. There are also those who were returned whose actions could not be found in a positive light. Were they corrupted by the opposition or is there more to it than we are able to see? We simply don't know.
There is a unique addition to the group discovered later when a 4400, Lilly Moore, discovers she was impregnated while in the future! This child's origins are uncertain at this time. Was she planted by the opposition in order to tip the balances in their favor or was she planned to help the 4400 with their purpose? This child, Isabelle Tyler, is presumed to have been fathered by Richard Tyler although this is never truly confirmed. She baffles many people in the months to come including her own mother who has a VERY unique connection with the child; she saves her parents life on more than one occasion and we also see her helping her parents escape from one Jordan Collier as he scares Lilly and Richard due to his unorthodox obsession with Isabelle. Is Jordan reacting to a suppressed memory that he took to a little too strongly? Perhaps he was meant to help Richard and Lilly guide Isabelle on the 4400 path in order to help them in their quest. After the child is born she is eventually brought back into contact with Jordan, and she is reminded of the feelings that he caused in her mother and gives him a false vision which ultimately leads to his demise.
Jordan is forewarned by Maia Skouris that he will be assassinated but he decides that he will listen to Isabelle instead. We later discover that Kyle shot Jordan during a "blackout" and is found to have an entity inside of him that is removed by Shawn. We can not be sure at this point whether it was the opposition or the 4400 faction that had Jordan killed but it seems as though it was the 4400 faction that revived and returned him with his vision.
Before, or near the time of Jordan Collier's death, the opposition sends some returnees of their own. 10 agents, who are against the 4400 and everything they stand for, who would have their consciences "downloaded" into specific people of our own time, one of these people being verified later as Matthew Ross. Another is speculated to be a man named Dennis Ryland. We find out that Ryland is, partially, responsible for the promicin inhibitor being developed and used earlier than intended on the 4400. This inhibitor is intended to counteract the abilities of the 4400 ultimately negating any positive changes they were meant to make. Due to the rushed introduction of the inhibitor many 4400's begin to get ill and close to 40 died because of this. Kevin is brought in and with Isabelle's help he is able to extract enough untainted promicin to give out one shot, minus what he hid from those around him for his own studies. This shot is given to none other than Shawn and he is able to heal the other 4400s after the shot helps him recover from this illness.
After the inhibitor scandal was discovered and the 4400 were healed we find that Isabelle has grown about 20 years overnight and introduces herself to Shawn. Unfortunately Isabelle's growth spurt has resulted in the rapid aging of her mother who is now dying. Isabelle attempts to commit suicide as a means of preserving her mother's life but instead discovers that she is able to heal herself to the point of reviving herself from death. This is when we see the actions of the future agent inside of Matthew take light. Matthew tells her that she is meant to do bad things and he was sent to guide her but she tells him that she does not want to do that and he gives her a substance and tells her that if she really wants to try and save her mother's life that this is the only thing that can hurt her, but he can't guarantee that it will work. She ponders on his words and the encouragement of her mother and decides not to take the shot. She struggles for a while to fight what Matthew has been telling her and eventually gives in. The opposition has now corrupted Isabelle and although she eventually kills Matthew she continues down this destructive path.
The 4400 faction decides it's time to step in and abduct the children from the present and reseed them farther into the past in order to counteract the negative actions Isabelle has made. Tom's partner, Diana Skouris is extremely distraught when she discovers what has become of her adopted daughter Maia Rutledge, now Skouris. She locks herself up in a Dream world created by returnee Alana Mereva and will not leave so Tom takes matters into his own hands. Tom was told that he was important in the events to come while the future was communicating through his son so he tempts fate and commits suicide as an attempt to contact the future and it works. He speaks with "Sarah" who is responsible for the kidnapping of the children, and she tells Tom that she will return the kids BUT he must do something he will not like and if he does not follow through it will cost him dearly. Sarah also tells him that next time they may not save him.
The agreement is made and the kids are returned directly from the future, now having never been in the past, and Tom finds them as well as his assignment "Kill Isabelle" and we see the very same substance that was given to Isabelle by Matthew. Tom confronts Isabelle about his mission and decides to wait until he feels he has good reason and in the mean time we see that Isabelle is meeting with Ryland in secret; she is supplying him with promicin which he is stock piling. Ryland is using this stock pile to secretly create super soldiers and he has also discovered that the Starzl Mutation seems to have a connection with promicin, apparently if a P+ and a Starzl have a child that child would have an ability. This seems to indicate that the catastrophe was originally very far in the future and the 4400 faction was hoping that returning them to the same location where the most people with the mutation could be found, would result in more babies being born with promicin in their systems.
Jordan is returned from the dead with a vision of the catastrophe, and his memory in shambles until Alana comes to help restore them, and Isabelle is worried. We see Isabelle admit to having given Jordan the false vision because of the way he made her parents feel and she confronts Jordan and apologizes, while he accepts her apology he tells her to leave and never come back which leads her to openly work with Ryland, who thinks he can control her. When Jordan steals the stock pile of promicin as a means of counteracting the vision he saw of the future Isabelle becomes infuriated and hunts him down destroying anyone who gets in her way. Tom finally takes out the syringe and means to use it. Her father ends up injecting her and she is stripped of her powers but Tom shoots her in the arm instead of killing her. We later see that Alana has been taken back by the future.
Alana was able to see the same things that Jordan saw as she restored his memories and after being taken to the future once more, she is "found" to have been sent farther back in the past and is speculated to have helped in the creation of a prophesy book used by a cult named the Wight Light group. Given Alana's ability, her knowledge from Jordan's memories and some possible information from the future she could very easily have started the group as a means to begin a foundation for the events to come. We see Kyle led to this book by his ability, Cassie, and he begins to study it and decodes a section with the help of Isabelle, who has now escaped from prison with a seemingly new attitude after the removal of her powers. They meet up with Jordan who takes them both in and begins to follow the book as well. We see Tom compromised by the Marked and another person, Drew Imroth, is discovered to be an agent as well.
Given what clues we have been given I believe the catastrophe to be biological and industrial in nature and that promicin somehow creates an immunity to the biological effects while the actions of the 4400 were meant to help eliminate some of the industrial origins, as well as improve some of the biological issues.
I believe this covers the major events up until now, if I missed anything let me know.
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