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(edit: Hey, so Safari is 2 steps per round. I made this a lot harder than it needed to be.
Changes for easy reference: changed main orders. De-cursed the 1/4 sub interactions now that bugs that only matter on step 3 don't matter. Added "and delay orders" everywhere.)
Sending Togekiss @ Scope Lens. Reflect ~ Chill
[end of Gyarados's turn] If Gyarados lacks Protection and Gyarados lacks Biding and Gyarados lacks a Decoy, use Dazzling Gleam and delay orders.
[start of turn] If Gyarados has Evasive, use Fly and delay orders otherwise and Counter the second instance.
[start of turn] If Gyarados has a Decoy, and Gyarados lacks Protection, use Seismic Toss and delay orders.
[start of turn] If Gyarados lacks Biding, and Gyarados lacks Protection, use Air Slash and delay orders the first instance and Dazzling Gleam otherwise.
[KO sub] If Gyarados is KOed, Chill.
Medicine
1x Potion
2x Hyper Potion
1x Full Restore
1x Max Revive
2x Ether
Balls
2x Quick Ball
1x Friend Ball
Field Effects: None
Team Abandoned Laboratory (1 Tech, 120 Battle Hours)
EP: 69 Capture Tracker: [ O O O ] Item: Gyaradosite Type: Water/Dark Abilities: Intimidate/Moxie/Mold Breaker Stats: 11/8/5/9/81 Other: Poison (3 Dosage), Toxin
Well, you prevented them from screaming. Great job. Iron Head~Iron Head
WHEN the step starts IF physical-returning move THEN Toxic the first time, Dragon Dance other times WHEN your turn starts IF Togekiss has Evasive THEN Skull Bash WHEN your turn starts IF Togekiss has Protection THEN Dragon Dance WHEN you are hit IF you are able THEN Avalanche
Protect ~ Chill
[start of step, once] If Gyarados' EP is at or below 40%, but above 30%, throw Ultra Ball and push back.
[start of step, once] If Gyarados' EP is at or below 30%, but above 20%, throw Great Ball and push back.
[start of step, once] If Gyarados' EP is at or below 20%, but above 10%, throw Poke Ball and push back.
[start of step, once] If Gyarados' EP is at or below 30%, throw Safari Ball and push back.
[KO sub] If Gyarados is KOed, Chilland look very confused.
Flow of the Zephyr is hanging by a thread...but you have the Gyarados on the ropes! Ice Fang~Ice Fang
WHEN the step starts IF physical-returning move THEN Toxic the first time, Dragon Dance other times WHEN your turn starts IF Togekiss has Evasive THEN Skull Bash WHEN your turn starts IF Togekiss has more than 15 HP THEN Stone Edge WHEN your turn starts IF you are able THEN Waterfall
Medicine
1x Potion
1x Hyper Potion
1x Full Restore
1x Max Revive
2x Ether
Balls
2x Quick Ball
1x Friend Ball
Trek 3: World Peace Engine
A secure storage facility, in the deepest reaches of the laboratory, awaits you at the lowest level accessible by the elevator. As you arrive, the readout on the elevator display simply says, "Weapon Development".
At the center of the room is a massive and inscrutable machine, connected to the ceiling with innumerable heavy pipelines and wires, that resembles both an egg and a tree. A terminal at the base on the machine simply reads, "Inverse Firing Sequence Complete." You have no time to ponder the meaning of this message, as the machine hums to life!
You step back and draw a ball from your belt as the immense egg-shaped base on the machine lurches and begins to slowly open. Releasing a billing fog with a pneumatic hiss, what emerges from within is—!
The referee's switching rule is On in this Trek. Before sending out, move both Boss Pokemon to the referee's Bench.
Boss Pokemon are always Enraged.
When one Boss Pokemon is captured: The other Boss Pokemon is removed from the battle.
This battle continues until the challenger loses; or until both Bosses are captured, fainted, and/or gone.
Camouflage: Steel | Nature Power: Thunder Wave | Secret Power: 50% chance to reset the defender's stat stages.
Conservation Reward: 1xMaster Ball (Release a Wayfinder caught in this Trek to obtain this.)
Wild Items (unlimited supply):
Power Herb
Fairy Gem
Dark Gem
Flying Gem
Eject Button
Red Card
Xerneas Level 4
Typing: Fairy Abilities: Fairy Aura
Requires 1 Tech to send out, once per battle.
—an unholy fusion of Xerneas and Yveltal! Wait, no, it's just a Xerneas holding a Dark Gem. Your dreams of mad science mixups will have to wait for another day.
[start of turn] If Xerneas has Protection, use Nasty Plot.
[start of turn] If Xerneas is to use Misty Terrain, and Misty Terrain is not in effect, use Taunt.
[start of turn] If Xerneas is to use Geomancy, use Snatch.
[start of turn] If Xerneas lacks Protection, and Xerneas lacks Evasive, and Xerneas has Poison, use Venoshock.
Xerneas and the Mega Gyarados from earlier have clearly had a pre-venture meeting about strategy. Maybe that's where the Dark Gem came from? Roar~Night Slash
Xerneas decides to turn your own tactics against you. Moonblast~Moonblast
WHEN the step starts IF Counter THEN ignore sub 4 for the rest of the step WHEN your turn starts IF Togekiss has Protection AND you have a Major Status THEN Aromatherapy WHEN your turn starts IF Togekiss has Evasive against single-target actions THEN Rock Slide WHEN your turn starts IF Togekiss does not have a Decoy AND Togekiss's team does not have Reflect up THEN Rock Slide
(Tricky Assist) Toxic
O ]
]
Togekiss), and keep 
Master Ball (Release a Wayfinder caught in this Trek to obtain this.)
Power Herb
Fairy Gem
Dark Gem
Flying Gem
Eject Button
Red Card
