The vortex sounded pretty impressive and intense. And I don't blame Rouge and Amy for being apprehensive about being on earth, specifically in this base.
Tail's, they surely are famous last words.

Yep, and they fight scene, maybe space it out a little but other than that, it was pretty brutal.
Sonic ended up with a broken arm.
Knuckles with some severe gashes to his midsection.
And both being plunged to their deaths.

Was the lower part of this ship submerged in water? IE did Robo Egg flood the other compartments to get rid of the other robots?

So the first part was all bloodshed, violence and gore. The poor earthlings of Station square. And Mr Preseidente, lol, poor Mr Thorndyke. I think it was very subtle of Metal Sonic to headbutt him like that when he could have been a little more ruthless without actually killing him.
But, he's been given an order to bring him back and he'd come through on that order. I'm wondering what the grand plan is going to be though and how it link Eggman and robo eggman.

Also, I love how sarcastic Sonic is at the most inopportune time. In fact; he reminds me of Jay. Knuckles the echidna, remind me of Cole, actually,maybe Shadow would be Cole.

Wow, that was certainly intense. Poor Frances and Danny, they obviously had no clue whatsoever, as is always the case in these types of event. And then Helen, had to say that, that's like the biggest no-no in the world, you never let on that you know the person the captor is intending to kill.

So, now she's a captive, and he's a robot, which means his only objective will be to destroy, and once he has, they'll be no further need for Helen.

Poor Helen lol

Ugh, the initial description of this Scrap Brain ship and subsequent inhabitants (all being robotic counterparts) sounds a little terrifying to say the least.
The ones that accurately depict a deadlier force of Sonic's friends sounds menacing, as you have written. And the fact that someone is down there, ready to activate this army into action is even more worrying.

Wat will happen next let's find out

Top notch