-( Story related, cannot be missed )-
The main antagonist all this time has been Ms. Risky all along! Fighting her in her hideout is actually the longest fight of the entire game. She can certainly take a beating. She has a repeatable pattern, making her also the easiest (to some extent). After jumping three times, she'll run to the opposing side (if she's on the left, she'll run right) and then shoot two different bullet types: a sticky straight shot that will explode after a bit, and a three-way spread shot. Following up with that, she'll perform a sword swipe from one side to the other three times.
Another three jumps and a run-to-the-opposite-side will see her perform a high jump followed by a diagonal three-way shot once more. Two more jumps and she'll perform yet another shot, then repeat some more acrobatic jumps. This time, she'll be on one side and start shooting a cannon downward from one side to the other. After performing this action, she'll disappear from the screen temporarily before reappearing, dangling on an anchor as it bears down on your location twice. You can hit her here or wait for her to sway back and forth, but the focus is to survive until she comes back down.
When she stops descending the anchor and instead sways above, just barely out of reach, Tinkerbats will swoop in and try to crowd you. You can pop these for hearts and magic refills if you're lucky. All you have to do is last until she gets done throwing her fire plumes and then she will float down to face Shantae at eye-level.
That's all there is to her fight. She can take a beating, so you will be getting a crick in your neck like Shantae from all of the hair whipping. Just as a notice, though... there is another trophy tied to this fight: