[Athenodoros]

Chomzloh, I am bored, so you get a short novel to lead into your pokemon, which fortunately will not need to meet any gyms.

You are standing in Sootopolis City. It feels like the end of the world, because two titanic forces are engaged in an epic clash in front of you. Then, suddenly, the gigantic, fearsome dragon you just awoke on the top of the tower flies into the mouth of the volcano, and everything slows to a crawl. The two pokemon, suddenly pacified, leave to go back to their respective caves, and after the dragon is satisfied that all is calmed, flies from sight. The assembled masses exhale, slowly, and all is silent for a time, until finally Steven, who stood and watched with you, turns and congratulates you, but you hardly hear. You are still stunned by the awesome display of power that you have just witnessed, and realise that before you challenge the Pokemon league, you will need to increase your strength. As it is, you still have one spot left in your party to be filled, and you decide then to fill it with a mighty dragon, just like the one which just saved the day, because you have so far struggled with mediocre Pokemon like Makuhita. You remember hearing myths about creatures of great power, so much so that they only battle now with legends, and make the choice to capture a Bagon, which you will train up to be a Salamence before the League. You decide to call it Iuppiter, after the great god of the sky, and in keeping with it as god of the sky, it must learn, and keep, Fly and Aerial Ace as soon as it gets its wings, and it must keep the powerful Dragon Breath, just like the Pokemon before. In addition, and as a true test of its mastery of the skies, it must defeat on its own the two titans from before (Kyogre and Groudon) after you defeat the Elite Four, before you tackle the true champion (Steven, in his funny cave), as well as soloing Drake, who arrogantly calls himself the 'Dragon Master', but must fall the great force you will now command.

Should it in this process die, however, you may not replace it because apparently the God-like Pokemon from before is insulted at your mimicry, and so you must leave an empty spot in your party as a mark of respect. This is unless Salamence was at a high enough level to take down Rayquaza by itself, in which case it can duel Rayquaza for mastery of the skies, which will cause Rayquaza to grant life once again to Salamence as its last act, as a mark of respect.

To recap:
After the last gym, you must catch a Bagon and evolve it into a Salamence before challenging Drake. It must know Aerial Ace, Fly and Dragon Breath. It must solo Drake, as a Salamence, and then go on to defeat Kyogre and Groudon before you challenge Steven, which seems to me to be the most logical finish for an Emerald Scramble.

If it dies, it must duel Rayquaza (One on One, no item use, although you may equip one) in the hope that the god-like Rayquaza will restore life to it as its last action, as a mark of respect. If it wins, this happens, but if not, you must leave an empty spot in your party for the rest of the game.