- The premise of "Green with N.V." is that a men's cologne is brainwashing men to leave their wives and girlfriends in search of "[their] true love", never to return. The sad part comes in when one steps in the shoes of the aforementioned wives and girlfriends who bought them the cologne as gifts, never suspecting that their significant other would leave them. This one wife and mother of two was tearfully devastated when her husband up-and-left on the anniversary of their happy marriage.
- In "Matchmaker", Clover discovers that someone is using shapeshifting technology to transform himself into the ideal guy based on numerous girls' specifications in order to stand them all up in a revenge scheme, and discovers Sam and Alex are taken in. When she tries to warn them, they brush her off, saying she's just jealous she hasn't found anyone to go out with and ditch her. Clover could only cry that not even her own friends believe her.
- In "A Spy Is Born Part 1", Mandy's entourage ditches her when it's revealed Sam is the most popular student at Beverly Hills (due to a miscount). It just goes to show, despite her money and popularity, Mandy has no real friends, just people who hope her popularity will rub off on them.
- In "Alex Gets Schooled", Sam and Clover were greatly saddened when Alex tells them her parents are shipping her Off to Boarding School because she didn't pass her classes. Not only was it heart-breaking to see the friends getting split apart, it got worse as the school was secretly a testing site for genetic experiments, and Alex gets mutated into a humanoid dolphin (although she claimed to like it, as the process also heightened her intelligence). Everything turned out all right in the end as it was then revealed that Alex did indeed pass her classes, her grades just got mixed up with Mandy's where she in turn gets grounded by her mother.
- In "S.P.I.", the S.P.I. organization competes against WOOHP and outperforms them at every turn. Jerry whoops the girls to the HQ to give them the bad news that WOOHP is closing down as a result. We get a shot of Sam's lower face as tears run down, pictured above, when they are told this harsh fact. Jerry tries to put up a brave front by saying this is probably for the best for the three girls, since if WOOHP is gone, they can focus on living peaceful lives and setting their own futures without having to deal with international crises. Despite this, Jerry was also broken up about WOOHP going out of business. All it means is that he and the girls may never see each other again. In the end, WOOHP is put back in business after it's revealed that S.P.I. is a fraud.
- The intended series finale, "Totally Dunzo". With all the bad guys caught and the evil gene eradicated, WOOHP is basically done. Jerry can retire and go back to England with his mother, and the girls can go back to being regular teens...and they are heartbroken about it. Still, they promise to return should evil come back...which they do come 2016.
- The girls all crying when they believe that Jerry is dead in "Evil Promotion Much?"
- Evil Graduation is surprisingly sad - Alex and Sam fear that they will grow distant from Clover and each other. Graduation can be a very sad time for people - especially since it's a massive change in their lifetime. The villain also peaked in High school, which results in him trapping his former classmates in the school. Cartoonishly evil? Yes... but oddly, understandable.
Tear Jerker / Totally Spies!