"Let's Play Soldier." The plot concerns a group of Joes in Thailand, trying to stop Cobra from harvesting hypnotic tree sap as part of that episode's Take Over the World plot. The Joes are helped by a group of Amer-Asian 'dust children' who are treated like dirt by the locals due to their mixed ancestry. At the end of the episode, a local man takes the four children on as business partners in his hotel and while one of the Joes thinks the kids would be better off coming to America, another says that what they really need is a home with people who love them and that they've found that in Thailand so why should they leave?
In the episode "The Gamesmaster", everyone has been led to believe Flint has been killed and Lady Jaye is in tears. Baroness puts a hand on her shoulder and offers comfort in her own way, along with a Rousing Speech.
Baroness: He was a good fighter, Lady Jaye, but think not of sorrow. Think of revenge. Revenge upon that accursed Gamesmaster!
In "Grey Hairs and Growing Pains", Zarana and Mainframe reveal that their affair in "Computer Complications" wasn't a mere fling, as she risks her life to save him and his friends.
Lifeline reconciling with his father in "Second Hand Emotions".
Lowlight is suspicious of Scoop being a Cobra spy throughout most of "Operation: Dragonfire" (he's right, but Scoop was tricked into believing G.I. Joe was responsible for destroying his parents' home and does his best to make amends after learning Cobra deceived him), but sincerely tells Scoop that he truly is a Joe after he helps save the day.
Duke reconciling with Falcon after he quits using drugs in "The Greatest Evil".