So we have a few stages for the adventure.
1. Arrive on airship, take in the sights, take down the defenders on deck (scouts and such).
2. The flocks of crow-ish birds . . . I want some sort of creepy white bird. Black birds are too over-used. Something cadaverously white. Know any good ideas? Anyway, the flocks take flight when the ship first shudders into movement.
3. Ship begins a slow maneuver to go into a spin. It will take a good three minutes before it's ready to dive.
4. Meanwhile, Pilus casts a projected image to talk with the group on deck, trying to stall them while being very congenial and curious. Pilus does this a lot. He's adept at defusing people's aggression toward him. If things turn sour, he'll offer not to kill them if they give him the Torch. They will undoubtedly refuse.
5. There are several large passages from the deck to the belowdecks area, but they'll be sealed and guarded. As the army tries to force its way in there, the ship will twitch to try to get them off. The lightning dragon comes out of the clouds and attacks.
6. A minute or so later, the ship has angled up sharply, and it begins to roll sideways.
7. If the group manages to get inside, and they probably will, the shock troops come out first, fighting in the corridors. Meanwhile, biomanced flying humanoids will emerge from hangars on the side of the ship, and will harrass anyone clinging onto the skin of the ship as it rolls.
8. The main badguys are in the area that would be the aftcastle on a real ship. The organs of the ship run down its central axis, with the 'breeding' areas toward the aft. Who knows where they'll go, but toward any of those ways, the approach passes a respiratory path.
9. There'll be a lot of defenders to get past, and there's only one main entrance to Pilus's control chamber. Sure, they could try to teleport in, but they'll probably need allies to get all the way in.
I'm thinking they'll have to retreat and wait for Pilus to be more vulnerable. They had a plan once to wait for Pilus to disembark his army and then strike. That'd certainly be easier, but they'd have to disable the airship's weapons of mass destruction, or else Pilus wouldn't really need to disembark.