Pokémon: Rest for the Wicked.
When Jessy and James end up stranded on an uninhabited island thousands of miles from the nearest City, Town, or even Village and with no hope in the world of getting rescued, they re-examine their lives up to this point, and over time their relationship.
Chapter 1
by 
Nemo of Utopia
"At least there's food and water Jessy, it could be a lot worse." James 'Training Wheels' Kolkata said looking out over the endless stretch of bright blue ocean which fringed their tiny slice of both Heaven and Hell rolled up into one on all sides.
"How can you SAY such a thing James!" His partner in crime since the age of five 'Chain Girl' Jessy (Jessica) Hakasumi snarled, anger concealing her slowly growing fear that they really WOULD be stuck on this large, but apparently undiscovered until their arrival, volcanic tropical jungle island for the rest of their lives. "When Boss Giovanni finds out we've crashed the 'Slice of Life' and been taking an unauthorized tropical vacation he'll drum us out of Team Rocket for sure!" Jessy snapped, but James just shook his head.
"Jess, I don't think we should be worried about that right now. Yes, the boss will be furious with us, and yes, he'll probably bust our butts back to Shoshinsha status, but only if we have nothing to show for our time here. This Island has Pokemon, ones no one else has ever seen. Boss Giovanni wanted us to catch rare creatures, right? What's rarer than something which Team Rocket has the only examples of in the entire world?" James said, trying to calm his partner with relentless logic...
As Jessy chewed on that thought her mind wandered back to how they had wound up here...