A general idea would be nice: maybe, just some tips, without spoiling the end?
A few later discoveries would reveal that the 4 ships are actually alien
The aliens did indeed board the ship, however they are surprised to find the ship crewless
The original crew had used the escape pods, none of the original crew are aboard the ship
The aliens have a passive aggressive nature, they avoid violence if possible but will not hesitate to defend themselves
The aliens aboard the 4 ships are quite similar to the changelings, though they are not the same
The aliens want to find out whether the ponies of Equestria are a threat, to do this, they analyse the behaviour of an individual of a species, once they understand common behaviours, they shapeshift into the individuals of a species and then land on the planet, where they can learn even more about the species by assimilating as an individual
The aliens have a problem though, they can shapeshift into a specific pony, but that pony will still exist, if they were to land on the planet without doing something to the pony they shapeshifted into, there would be 2 very similar ponies which would raise suspicion and blow their cover
Something has to be done to the ponies they shapeshift into...
Fortunately, the aliens run into complications...
// I feel like I've butchered the story I had planned there, but that is an outline, we don't have to follow it though...