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Tear Jerker: Area 88
In the manga, when Shin and Mickey fly over a Bedoin camp that had been slaughtered by anti-government troops. Shin was mortified, particularly at the sight of a dead woman clutching a dead child.
In the manga, we see a flashback of Saki weeping after Soria dies giving birth to Rishar. He lovingly holds the newborn Rishar with tears running down his face.
In manga published in Animerica, Saki is deeply distressed as an injured Rishar clings to life in the Area 88 infirmary. Saki admits that he "truly will be alone" if Rishar dies.
In the manga, Tracy's exposition to Mickey on the tormented man he'd become after the Vietnam war.
Toward the end of the manga, Greg's death scene. After his A-10 crashes near Asran City, he finds a little girl whose mother has just been killed in the fighting. The crying girl accidentally shoots him with her family's gun. Greg is not angry, and he tells the little girl that she will be a good mother someday. He dies peacefully, smiling.
Near the end of the manga, a dying Abdael tells Saki about the real reasons why he instigated Asran's civil war: to develop Asran's medical technology through foreign capital so that a treatment for Soria's blood cancer could be discovered.
Also, Saki's suicide near the end of the manga, after Abdael reveals the truth about Soria and the roots of the Asran civil war. Saki admits that the Asranian people would not accept him after his role in the civil war. He carries Abdael's dead body into Soria's tomb and shoots himself as a horrified Shin looks on.
In the manga, Kanzaki's account of his mother's suicide is a tearjerker or a source of nightmare fuel, depending on your perspective.
Near the end of the manga, Mac learning that his daughter Miriam has died.
Boris's death in the anime and manga. The manga is more heartbreaking because both Shin and Mickey are screaming at him to save himself, and he doesn't.
In the OVA, seeing Shin burst into tears in his quarters, lamenting his involuntary servitude at Area 88.
The final battle of the manga when Mickey dies. Just for the fact he died trying to save Seilane from her wreckage is pretty heartbreaking.
Actually, it was the other way around. She ran over to his wreckage after his F-14 crashed on the runway. They were both consumed when the wreck exploded.
Mickey has the unfortunate problem of fighting Patrick Reed, one of his wingmen back in Vietnam War fighting for anti-government forces as a mercenary. After defeating him, Patrick tells Mickey that he wants badly to go back to Oklahoma, highlighting the problems military personnel back in regards to integrating back to normal lives.