Plan: Aegis
[X] 0: Shuttlebay (+20,000 Tons)
Shuttles are the only force multiplier option on the list. If you need the ship to respond to another event, you can leave a couple of shuttles behind to support and extract the inspection team(s). Have shuttles you can launch sneak attacks on pirate bases while the ship draws attention away. Need an impromptu listening/observation post, deploy a shuttle.
Shuttles are an easy item to upgrade in the future as well. Fly the obsolete models off the ship, fly the new types on to the ship.
We want shuttles.
[X] 1: Transporter (+10,000 Tons)
When you need to pull civilians out of an exploding ship, rescue hostages or covertly insert operatives, nothing else will do.
[X] 2: No Cargo Bay
This one is nice, but probably not necessary. Cargo Bay for hauling supplies, storing contraband, holding rescues, making emergency supply runs... Would all be great capabilities, but can also be performed by civilian vessels.
[X] 3: Brig (+10,000 Tons)
We are building a customs and police vessel, it will be collecting involuntary passengers. Those involuntary passengers will need to be housed in appropriate accommodations.
[X] 4: Tractor Beam (+10,000 Tons)
Stabilizing out of control ships, "non-lethal" method for stopping fleeing ships, rescuing stranded shuttles from the crevasse of an ice comet, all things we need a tractor beam for.
If I understand this phase correctly, this should give us a 110,000 ton vessel.