Looker

Let's take that idea and bring it into the canon:

Looker is on a mission (a regular, boring one) in Hoenn on account of reports that environmental terrorism is being suspected of being planned by some of the locals (which, of course, turn out to be Maxie and Archie). Looker doesn't believe his presence there is either needed or useful, so he's pretty bothered by it. When the standard plot starts to kick off, Looker (as he does in DPPt) decides to help you, given that he failed in his mission to prevent the forces at work to flood/dry the world.

While he helps you on your quest inside the Magma/Aqua bases, the story continues on as per usual. This can be an opportunity to build on Looker being in this game, since they're both fairly lengthy dungeons.

When the story comes to a head and Kyogre/Groudon start fighting, things happen as per normal. Looker though, before you do, hauls ass over to Sootopolis City to try to stop both Maxie and Archie, who have their respective orbs (forgive me if I'm not great on the story. I haven't played Emerald in some time), which Looker thinks can help quell them both. You, when you get to Sootopolis, meet up with Looker, who has incapacitated a few of the Aqua/Magma grunts but is stopped by an Aqua Admin and a Magma Admin named Saturn and Mars respectively (think of their hair color. It fits well.) You defeat them both in a double battle alongside Looker (who of course has his Croagunk and a few other 'mons rented to him by his employer). Looker gets your back and stops reinforcements from both teams from getting to you while you go on to confront Maxie/Archie and observe Rayquaza do his thing.

After the fight and all is said and done, the people of both teams are accounted for in cuffs (sans Maxie/Archie, who jammed as soon as they could and Saturn/Mars, who managed to fight through the police and escape) and Looker remarks on the escaped felons. One of the things he says about Saturn and Mars is that, "I don't know why I get this feeling, but I just know I'm going to see more of them in the future, and they're going to be trouble. Not in this fine region though; I think we took good care of it and its inhabitants, <player>. Well... it was mostly you. I can't thank you enough."

You can go on and have him do stuff in the postgame if you'd like, though. I tried to make it as not-fanfiction as possible. Clay can be the judge of that, though, since he's got the thing against fanfiction.

god, I know you wanted to integrate the whole Jirachi thing, but the canon is that Aqua and Magma totally disbanded after the final event. Just as well, Maxie and Archie kindof did a heel-face turn and are more or less not bad guys anymore after the Rayquaza event.