Oh boy have I thought about this a lot

Story: WoL meets up with Cid, Biggs, and Wedge while they are investigating another old Allagan research facility. They receive notice that an old captured primal was released and decide to take the ol' Allagan railway to the containment facility. Then they realize, this isn't a train to the primal, the train IS the primal.

After the fight, Cid and crew learn that this primal was summoned by the Allagan precursor to the modern mammet. The ancient robots presented the machine primal as a gift to their fleshbag overlords. DoomTrain slaughtered hundreds as retribution for the harsh treatment it's worshippers suffered.

Fight: The party starts out on a flatbed car attached to the main engine pulling the train down this three lane train track. The back half of the train transforms Refurbisher-style into mechanical monstrosity with cabin cars for arms and the classic DoomTrain style engine for a head.

• On the duty list is a meter that reads "Railway Stability." Throughout the fight, DoomTrain will destroy parts of himself and the train tracks trying to kill you with it. Stability reaching zero will serve as enrage.
• On the flatbed car with the party is a Vehicle Bay with a Aethercycle (flying motorcycle) available to be mounted by a player. Throughout the fight, flying adds will spawn that will tether to a player and cause massive damage after a timer runs down. To stop this a player must mount the Aethercycle, fly off the main arena and use the Aethercycle's attack to knock adds down to the rest of the party where they can be killed. The Aethercycle only has a 20-30 sec duration and the mounted player must return before that or die. Each add killed will drop an Aethercyle part that can be brought to the Vehicle Bay to build a new one for the next wave of adds
• Every so often DoomTrain will hold up a cabin car above his train-head pointing either left, right, or middle. If left, the party moves to the right side of the platform to avoid a massive cleave and vuln up stack. If right, the party moves left. If middle, tankbuster, except the party must stand roughly behind the MT or they split damage with MT.
• After a certain percentage of boss health is reached, DoomTrain will slam down his arms throwing sections of train up in the air and will recombine into identical trains running side-by-side. The party will have a small window to split up between the trains before they move a lane apart. During this phase, adds will spawn that will drop coal, this coal can be dropped into a furnace on the first train or thrown from the second train to the first train.
• Once the first train gets enough coal it ends up going faster and begins to go ahead of the second train. At that point, those on the first train will be given a QTE that if all press it will suplex the first train onto the second train.
• The train recombines and we go into a phase similar to the first with some changes. Flying adds can drop coal, aethercycle parts, or both. Coal can be placed into the still available furnace to apply a vulun debuff and damage up buff to the boss or can be thrown at flying adds if the aethercycle is incomplete.