Forgive me for misusing any terms. This is a subject I'm not knowledgeable in at all aside from doing some online research.
The ship has two moon pools and a drilling rig that lowers the drill through one of them.
The previous crew came across an alien object floating around 500 meters underwater.
The object is spherical, at least $2,500$ ft in diameter, and has a thin outer layer, a shell, with a very small comparatively (maybe less than $20$ ft in diameter) upward-facing vent leading into it.
The entire object is large in volume, but not in mass. Aside from the thin shell which is filled with fluid, and a small inner core that holds its "brain", the rest is likely mostly hollow or filled with very not-dense material.
It's never quite explained in the novel what the whole object is made out of, but the object can control its buoyancy through venting ballast from its mantle (I'm likely misusing these terms horribly), perhaps through the vent in its "crust".
The research vessel discovered the object. After studying it they came to the conclusion that they had to stop it from surfacing completely for various reasons and that they didn't have much time.
How I've been thinking about executing this is that that the crew somehow attached a long metal beam to their drill and lowered it vertically through one of the moonpools and down into the alien object's small vent so that the beam would turn horizontal and end up "stuck" inside the object's mantle like a T-bar clasp on a necklace. Then they would lift the entire object up by the drill line to lay the vent flush as possible against the ship to. Maybe they packed in some material around it as well if the bottom of the ship wasn't flat enough to make a seal.
The crew didn't have a lot of time to come up with something more elegant or use any objects besides what would be found on a research vessel during an expedition. Maybe the metal beam was cannibalized from some other equipment.
For the ships I mentioned above, the Aurora Borealis is around 655 feet long, and the Chikyu is around 690 feet long and has a displacement of 57,087 tons. I imagine the in-novel ship could be around 700 feet long and similar in displacement to the Chikyu. The alien object again is around 2,500 ft in diameter.
The primary question would be if is this feasible or realistic at all and if so, does it mostly depend on the alien object's mass? Can the object be light enough that the ship could feasibly try to "trap" the alien object against itself without breaking or capsizing?
Or does the sheer volume of the alien object alone make this unfeasible?
If it is possible, would the drill line(?) and/or the drilling derrick of the vessel need to be reinforced in any way (since I assume sea drill lines(?) aren't meant to carry objects like the large metal beam I imagined them using to lock the alien object in place.)
I know vessels like this would likely have cranes as well, but I'm not sure the cranes would go deep enough given how deep in the water the alien object is when the ship found it. The drill setup might also be more precise I suppose.
I know a lot of factors are missing, like the material the alien object's crust is made out of, how thick it is compared to the rest, what the fluid is in the mantle, etc. But I'd be willing to adjust all of these factors to make what the research vessel's crew does feasible.
I know very little about physics or ships or deep sea drilling, so I apologize if I'm not giving enough information. :(
I might also be overlooking some things that are very obvious, so feel free to point anything out.