The reason for The Walking Dead season 9's darkest moment was explained in the latest episode, "We Are The End Of The World". The incident with the Whisperer baby that was almost eaten alive last season was engineered by Alpha (Samantha Morton).
In a season 9 episode, the Whisperers arrived at the Hilltop to have Lydia (Cassady McClincy) returned to them. Also present at the scene was a baby, which threw a wrench in Daryl's plans. Daryl (Norman Reedus) had no interest in negotiating with the Whisperers and was perfectly willing to have them all gunned down - until he saw the baby. When a herd of zombies were attracted by the child's crying, Alpha expressed no remorse as she made the decision to leave the baby behind to be eaten by the zombies. Luckily, the child was rescued by Connie (Lauren Rindloff) and taken in by the Suttons.
The Walking Dead season 10, episode 2, "We Are The End of the World" focuses on the Whisperers and a conflict brewing between the child's mother and Alpha. The woman is deeply haunted by what happened, and as flashbacks reveal, Alpha is responsible for what happened to the child in more ways than just one. Not only did Alpha nonchalantly give up the baby, but it was she who put the baby in that situation in the first place. She told the mother to bring the baby with them when they went to Hilltop.
This episode succeeds in driving the point home that Alpha is a cold-hearted person devoid of any sort of moral compass. What's worse, Alpha is a selfish villain. Her scenes with Beta (Ryan Hurst) expose Alpha's hypocrisy. While she excepts her followers to give up their loved ones without question, Alpha has yet to do the same with her own daughter. She knows that Lydia is her weakness and that weakness may very well be her undoing.
Alpha's monstrous and heartless nature was on full display when she showed that she didn't care about the baby, but "We Are The End of the World" takes her cruelty to a new level. Clearly, Alpha used the child as a defensive measure. She must have known from the start that the people of the Hilltop would hesitate before bringing harm to an innocent child. So essentially what Alpha did was take advantage of their compassion. An innocent baby was just a means to an end for Alpha, and that makes her willingness to sacrifice the child even darker.