Story related and unmissable.
This boss battle is either a total pain or a slightly average pain.
When you're given the option
you basically set up the difficulty.
Choosing him will give you 2 additional partners when the battle starts and choosing her will give you one.
Once the battle begins you'll see more Dokugumon and, like the first boss battle, there are 2 sizes.
The big one should be your main target first because killing it
Other than that taking the other Dokugumon out is easy since they're laughably weak, doubly so if you're using Vaccine type Digimon.
If you beat Arukenimon before freeing everyone that's fine too, the battle will end immediately, but the struggle is much more real.