I understand that there is a deeper story going on and that narrowed the focus on three or four characters which means some were lost in the shuffle.

So in the interest of saving people the trouble of finding the posts I'll give a short rundown here.

Just before the military attack Jesse was suffering a sort of mental break which centered on how the government treated her mom. This break triggered repressed memories causing Jesse to remember that the last time she saw her mom MI6 was taking her away to a meeting of sorts.

Then Jesse was taken from the lady in whom's care she'd been placed by her mom and it was done like a military raid.

Jesse recalled being taken somewhere and having medical tests run while she was under heavy drugs then discarded when someone said she was a failed project.

It was shortly after these revelations that the Head Quarters came under military Siege 

She heard the demands and how the government decided that Meta could be forced into Slavery or Lab Rat status without any recourse except compliance 
That reminded her of how she's been treated her entire life; as a possession not a person which fed into her triggered memories.

Now she's sort of runaway to search for answers

Oh an she's changed her callsign to "Star Child"