I think you are

performing your job as secretary ship pretty well though...

That's not true!

Are you lacking something?

Are you really sure?

If I become the secretary ship,

That means you won’t be the secretary ship anymore. Is that okay?

It's fine!

I'm the mother ship after all! Both お艦 (ship) and お母ん (mother) shares the same pronunciation.

What is that supposed to mean...