-The evil secret society, which Leonard Testarossa is one of the major leaders of, fully reveals itself soon after the end of TSR's OVA followup. They are actually a Super Ultra Powerful (tm) military force, and easily crush their opposition; the good organization Tessa and co. belonged to is instantly wiped out (except for Tessa and her sub, who escape) because you know, secret armies of mercenaries are always so much more powerful than nations' actual armies, right? I've always greatly disliked the stupid "secret army which is stronger than the normal armies of the nations of the world" idiocy, and that's sort of the plot of the rest of the show, Sousuke and Tessa's people having to save the world all on their own as the rest of their organization is gone and the normal countries are no use, of course... sort of like the useless adults in your average "kids have to save the world" series, I guess.
-Naturally, the school-life side of the show vanishes with the attack and does not return. The characters from school are very rarely seen from this point on.
-Chidori is kidnapped during the assault, as Sousuke fails to protect her. She stays kidnapped for a long, LONG time. Like, pretty much until the very end of the series long, after they are separated. The main plot turns to Sousuke's efforts to rescue her all on his own -- he is separated from any help. I hate "rescue the kidnapped girl" plots! It's such an awful crutch of a trope... it's sexist and stupid. They made a great pair, too. Why did the author think that separating them long-term was a good idea? It wasn't! And her appearances go down for sure as a result, too.
-There's a short arc where Sousuke goes to Vietnam (or is it Thailand? I forget) and meets a few people there, most importantly a girl. He learns that she is also a Whispered, then she is murdered in front of his eyes as a standard "fridge the girl in order to get the MC angry" terrible plot device. Sousuke then sets off on a solo quest to start saving the day, any thoughts of doing otherwise dashed by the jerk villains. And yes, the girl stays dead, unlike the other "dead" major-ish good character in this series.
-Tessa and her sub are the only survivors of the good organization. She tries to save the day with only her crew and noone else, but after some struggles and efforts to fight back against Leonard's super-powerful group, is eventually betrayed by a high-up traitor, none other than Kalinin, and ends up losing the sub, though a good amount of the crew survives to continue fighting. She does survive though, and they do what they can to stop the badguys. Tessa gets tougher; this is one of the only things I liked post-TSR, Tessa's cool (mostly). Tessa's goodbye to her submarine that she designed is kind of sad, too.
-Leonard wants to start a nuclear war because evil supervillain stuff ('make a new world', etc.). Kurz seems to be killed in one of the battles. Meanwhile, Leonard has gotten an alternate personality, Sophia, to sort of take over Chidori, who is working to help his cause. The Whispered thing is from a woman called Sophia who died 18 years ago in an experiment on Leonard's island base. This set off some weird time loop thing, I think, which allowed for the creation of all the tech Whispered has led to. Kaname refuses Sophia's entreaties to destroy the world and bring it back as a new world, since apparently she could do that, and instead sticks with the world as it is.
-Sousuke goes to stop him, finally re-united with his mech again. Mao goes to stop the missile launches (which are launching from somewhere far from the other battle), and does (after some fighting), but one missile gets away. The one missile is aimed at the island where Sousuke, Tessa, Leonard, etc. are... but no civilians.
-Sousuke defeats Leonard, but is having trouble shooting him. In the final confrontation in the series Kalinin betrays Leonard too and shoots him (before Leonard can hit a button that would have probably blown up the base). Then Sousuke finally rescues Chidori (she's back to her normal self), but they are immediately separated. Tessa and her troops leave after hearing about the nuke, but she takes Leonard's body with her. Kalinin tells Sousuke that he is his father (it's true). He goads Sousuke into a fight. Sousuke can't kill Kalinin because he's his father, but Kalinin dies of other injuries anyway. Before dying, Kalinin tells Sousuke he's a good person and should live on.
-Kalinin also says that he turned to Leonard's side because he wanted to 'bring Sousuke and myself back to where Irina and my child [Sousuke as a kid] were'. Chidori kind of dashed that dream, but I'm unclear on how it'd have worked anyway. First nuclear war, then Chidori does something with Whispered powers, then... a new world where things are better? Why is the nuclear war step needed? (Real answer: To have a threat the heroes need to stop.) This probably is explained if I read the series more carefully, but it's probably not worth the effort... it's not like this is a great story.
-In the end, Al activates the Lambda Driver on his own to save Sousuke from the nuke blast. Leonard and the other villains are killed and/or defeated, and it is revealed that Kurz is actually alive, so Sousuke, Kaname, Tessa, Kurz, and Mao all manage to survive the series, unlike lots of minor characters of course. Obviously Kaname and Sousuke end up together, to try to return to regular life in Japan. They kiss, the end.
-Oh, apparently with no evil group there's no need for AI mechs or something after they've won... because nations can't just build them themselves? I don't get it. There may be some bad explanation for this (connected to the whole Whispered thing), but I kind of doubt it makes sense. Or maybe it's just the goodguy group that's not needed, and not the mecha thing in general? Maybe the novels explain this better, the manga sure doesn't. 'Whispered is sort of gone now, but Sophia's still in Kaname's head but not evil now' or something like that.
