I was running a GURPS Fantasy game once where the PC's were able to look into their past lives and the party wizard discovered his Raccoon familiar was actually his wife from another life time. For a brief moment he remembered the connection and the explanation why the familiar chose him was the connection. The party eventually looked into transformation magic and turned the Raccoon into a woman and the two of them started the relationship back up again. Weird? Neh?
Back in my college years I had a long period of interesting 'twist' plots like that in my games. Stuff like a Ninja College Game (inspired by Ninja High School) where the players discovered that all the badguy NPCs were exboyfriends of his one girl who was mentally dominating them and changing their personalities into monsters. She wasn't doing anything evil, it was her exes. Even though she benefited from their deviltry. I also ran lots of variant plots like this were hidden relationship and drama was behind the NPC actions. Another game had a Sailor Moon plot where the PC's were hosts to magical animal spirits. They had a reoccurring NPC raven themed guy who helped them out and seemed to be hitting it off with one of the female PCs. The catch? He was a SHE! The spirit animal granting her super powers changed her gender when she was in her powered up form. And worse, she was the sister of the big bad of the setting. (Another powered kid, but much more darker bent in mentality.) Boy was that fun.
I call this style of relationship twisted "Tabloid Logic". I've heard others refer to it as Shōjo/Shōnen plotting. But for those who don't watch Anime, Tabloid Logic works well enough. It's used in comic books as well. Scarlet Witch liked Wonderman, but that relationship didn't work out, however Vision who had a copy of Wonderman's mind DID date and marry Scarlet Witch. And even weirder she had children thanks to her magic altering pieces of a demon's soul. Or once Supergirl (the non-Kryptonian one) dated Lex Luthor in a younger clone body who was pretending to be his own bastard son. Ya, very soap opera...very tabloid logic.
I support this type of drama plotting in games because it does a few things:
a. It throws the PC's off on some of the more secret elements in a game. Sure, I'm fine with them picking up the general plot, but there always has to be and edge to NPC actions and that edge needs to tie back to the players.
b. It ups the stakes for the players when NPCs or even their own back history tied directly into the action and conflict of the plot. It doesn't always have to be revenge, Batman plots. A better twist would be say Catwoman secretly gave birth to Batman's daughter, and the girl is the new Robin...only no one but Catwoman knows it yet.
c. It's great for the classical ass pull. No, I'm serious. If you are a 'from the hip' GM like I am, sometimes you have to use Tabloid Logic to fix a plot hole. Mind you, take a breather, get a soda, and think about how that impacts the story at large. But why not? It's interesting and will take the PC's many game sessions to learn the secret, resolve it's conflict, and then sets up for later adventures.
I have a few general guidelines on pulling out Tabloid logic though.
Don't squick out the players. You can disturb them, put them on edge, even make them a little embarrassed. Just don't get gross and overly descriptive on weird relationships. Let them work out the implications on their own. Hint, guide, don't slap it in their faces.
Always have it tie back to either the Players or a major NPC. No random strangers show ing up in the plot. Now if you are taking the time to establish a new NPC this trick is great, but make sure you put enough logical (semi logical) ties to the current dynamic so it works.
Keep a rough relationship diagram on a scrap piece of paper or your GM notes. It doesn't have to be Smallville level complexity, just a reminder for the twists and connections you need.
Once done with the new link, crank up the Telenovella music, have his Evil Twin show up and marry the player character, then pass the popcorn.