I'm guessing the ending was made as ambiguous as it was to let fans judge for themselves what happened when Lucy confronted the soldiers. Either she was killed or returned to Kouta with the loss of both her horns from the fights she endured.
The little girl who was molested almost gets raped again, this time by some Diclonius hunter.
Eventually, as this stuff is prone to do, the plot becomes a battle for the fate of the world and mankind.
Also as this stuff is prone to do, bigger, badder , and sadder sob story origin Diclonius are revealed.
Lucy dies to save humanity but there is something weird in the last chapter like oddball twins appear that seem to have some type of affiliation with Lucy. I don't remember exactly what it was as I read this all years ago.