Episode 4. The ball really gets rolling thanks to its reveal of the past and the truth about society.
Episode 9. It is revealed that Shun is transforming into a Gouma, which is clearly not going to end well for him. We also get our first glimpse of a Fujoneko.
Episode 12. Satoru's grandmother and head of the Ethics Committee explaining a few things such as: why they get rid of the children to asking Saki to be her successor.
Episode 15. Maria and Mamoru are MIA. More importantly, however, it is revealed that Squealer has overthrown and lobotomized the Bakenezumi queen, keeping her alive solely for her breeding capabilities. The now unified colonies have also made drastic advancements in its military and technology, surpassing what exists within human settlements. And Satoru and Saki fear that Squealer may be planning a conquest of the human settlements.
Episode 18. While Kiromaru survived the war, his colony (the Giant Hornets) were completely erased from the earth through the use of a cantus user controlled by Yakomaru. With no other colony left in his way, Yakomaru declares war on Kamisu 66 by killing civilians in the middle of the village's Summer Festival. While the village still stands, two of the board members were KIA and Tomiko mobilizes the village for war. Above all, Maria appears near the end of the episode. There, she reveals an additional reason why she left Saki: she wanted to have children, a dream that would have been biologically impossible to achieve if she stayed with Saki. Definitely Foreshadowing who will be Yakomaru's trump card...
Episode 19. While attempting to rescue survivors in an Abandoned Hospital, Saki and Satoru find out that Yakomaru's trump card is none other than a 12 year old Akki. Any further explanation on why that's bad news for our protagonists need not apply.
Episode 20. Even though Saki and Satoru barely avoid a brutal death, a blast from the suicide-bomb fish mutant ends up separating the two. After meeting up with a mysterious young survivor, Saki returns to see Kamisu 66 almost completely erased from the Earth. The true Wham moment, however, comes near the end of the episode, when Saki finds her mentor Tomiko seriously wounded in the Sage Academy, which has been transformed into a makeshift hospital. Knowing she doesn't have much time left before Yakomaru's forces (his Akki included) finishes the village, Tomiko hands over her role as the head of the Ethics Committee to Saki. Shortly afterwards, she orders Saki and Niimi (her assistant) to leave her behind and sits in her bed awaiting her fate.
Episode 21. Saki and Satoru discover that the Akki is in fact Maria and Mamoru's daughter (son in the novel), meaning that Yakomaru murdered them and brainwashed their child. The Akki then kills Shisei and most of the rest of the village, with Saki and Satoru barely escaping. They then find out from another survivor that Yakomaru has kidnapped all of the village's children, intending to create an army of Akki to take over the world.
Episode 25 reveals the dark truth behind the existence of the Bakenezumi. Satoru reveals that they have 23 pairs of chromosomes, just like humans. Why is that important, you may ask? Simple: It turns out that when Death Feedback was introduced to people with PK, those with PK suddenly viewed those without PK (the hunter-gatherers and the commoners mentioned in Episode 4) as threats to their authority since those without PK do not have Death Feedback. To remedy this, they forcibly deformed and transformed those without PK by inserting naked molerat genes into their DNA. The transformation was so drastic that a person with PK killing the deformed PK-less person would not trigger Death Feedback. Learning about this sick, morally reprehensible process is all it takes for one to lose whatever sympathy he or she had left for the human society (with the exception of Saki and Satoru). The kicker? Most humans don't even know this since the ones in charge kept it a secret.