really the story line was simple,
SPOILER ALERT!!!!!!!!!!!
Alex was a scientist that discovered what exactly blacklights plans were, decided he wanted to expose them and put a stop to it, he stole a vial of the virus. They tracked him down and cornered him in central station and busted the vial thus spreading the infection all throughout manhattan. He as shot and killed, the virus entered his body and became alex.
Alex was dead, the virus just mimicked him and made himself believe he was alex.
Elizabeth was a girl in Hope Idaho, The first testing grounds for the virus that got out of control and they wiped hope off the map and reported it as some accident.
She was the only person the virus didnt horribly mutate and kill.
She somehow got pregnant while infected, She gave birth to a baby. Codename Periah. Aka the final boss. The stran of virus alex released was taken from elizabeth, thus making her alex's mother in that sense.
The whole point of the story was alex was trying to uncover what happened to him, Elizabeth, Hope Idaho and stop the virus.
You find out what happened to liz and hope through the web of intrigue, You find out about periah and alex through the main plot. theres alot more to it thats a little more complicated than this, but thats the jist of it.