Flashback!
When Terra asks about why they have so many pokemon eggs and if that was why they were in the cave for so long, Nathan nods.  "Yup.  There was a talking Arcanine in there guarding them.  No, I'm not kidding.  The eggs he's guarding are all species that are either endangered in this time or will be in the future.  The ones he gave to us are all endangered in our time, and the rest we left with him aren't.  Shiva has a Minicorn and a Flabebe, I have a Dratini and an Absolite, and Heart...*looks around to make sure Juni is out of earshot*...has the Legendary Winged Mirage of Fire, Moltres."  (Cue surprised questions from Terra?)
It's a straightforward and frank explanation. Â It doesn't have to be any more complicated than that, really.
Present Time!
Nathan is so, sooooo relieved when the lurch brings them back to 2017.
Ditto and Gallade had both remained outside of their pokeballs while attempting to trek through the thick jungle.  Except as soon as Ditto settles back into the present time, it instantly Transforms. Â
Instead of a Flygon, it's now a Lunatone once again!
Now then, as soon as Nathan gets his bearings, he checks on the Dratini egg to make sure it's okay...and also still there.
And it is, presumably!  Phew, no paradoxes...Nathan knowing everything he does, time travel was a rather...stressful experience for him, to say the least.
Though since the Dratini egg is there, that also means...
Terra says it as Nathan is thinking it. Â Yup, they still have Juni captive.
"...everything's okay on my end, Terra. Â We should probably turn Juni in to the authorities sooner rather than later. Â The sooner we do that, the sooner we can relax a little. Â Everything okay on your end, Detective Thrawn? Â We have a few Teleport users if we need to reach Cress immediately, or we could just walk back."
Also, assuming Bill gave Nathan his number when asked for it, Nathan will call/text Bill.
"Bill, we're back. Â We're probably going to turn Juni in to the authorities before we do anything else, and we'll probably have to take it easy for the rest of the day. Â Do you need us to return the watches?"
As for the pokemon Nathan will keep on hand...that'll be Gallade, Ditto, the Dratini Egg, Calam, Swiftfire, and Snivy.