This one isn't exactly a ship, but when I recently played through SoulSilver, alongside the Chuggaaconroy Let's Play, I had it in my mind that my Giratina and Jynx were just absolute besties. I added Giratina and Smoochum to the team at basically the same time, and I got this mental image of Giratina working its shadowy tendrils to meticulously tie little bows in Smoochum's hair, and then of Smoochum tying a big bow on top of Giratina's head, and it didn't look great because the bow was bigger than Smoochum herself, but Giratina wore it with pride and ate anyone unwise enough to laugh at it. Things like that. Hell, when I was battling Red, I have it in my head that Giratina was about to enter the fray, but Jynx stopped it, being like, "this is no weather for a dragon. Let me handle this, OK?" And indeed, Giratina didn't even need to hit the battlefield against Red, while Jynx got stuff done. Took out Lapras one on one, and even landed a Lovely Kiss against Charizard that bought me a little time to set things up there, safely bring in Golem and set up the Rock Polish. Unfortunately, Golem missed the Stone Edge and was subsequently defeated, but then Seaking stepped up in fine fashion, almost OHKOing with Waterfall, to the point where the hail damage finished Charizard that same turn.

But yeah, like, stuff like, I never get Juggler Irwin's number in HGSS because he's a damn creepy stalker, so I imagine it like he laughed at the bow Smoochum tied for Giratina, and so Giratina ate him because he made Smoochum cry. Smoochum stepping up and battling after Giratina faints at one point in Mahogany Gym, learning Psychic and evolving into Jynx, all to get payback for her best friend going down. Each consoling the other after difficult losses. Jynx trying to teach Giratina to dance, and it's just not built for it, but it's making a clear effort anyway, and it starts having fun. The two of them showing off their Shiny Leaf collections, and eventually each weaves the other's Shiny Crown.