Okay, my understanding was that the scientist impregnated the main character on purpose to produce a child that was bonded to a specific whale (Scarlet) through inherited nanites. He had done this before and had other children who were bonded to other whales. These children were being used to get their whales to do various things, including military aggression against opponent nations. One child/whale pair had been specifically used to attack and sink the submarine of an opponent nation without leaving a trace of the aggressor nation's involvement (devious!!). The MC doesn't want her daughter used this way, so she takes her to Scarlet, who joins the daughter's consciousness to her own (both consciousnesses now inhabit Scarlet's body), leaving the daughter's dead body behind. The MC, who has exhausted herself to save her daughter (at least her consciousness), dies content, knowing that her daughter has found a safe harbour.
Okay, when I write it out this way, this is an amazing story!! Unfortunately, it didn't really come across in the way it was told. The MC is too distant and there are not enough details to make sure the reader is getting all this information at the right time, as can be seen by the confusion in the various forumite comments.
To sum up, I liked the plot, but feel the presentation needs more work.