How to set second step as active step in Material-2 stepper?

Add a reference to your stepper e.g. #stepper and after the view initializes, set the selectedIndex of stepper to 1.

In your Template:

    <mat-vertical-stepper #stepper>
        <mat-step label="Agreement Preparation">
            <p>Agreement preparion is intiated by our side </p>
        </mat-step>
        <mat-step label="Ready for Biometric">
            <p>Agreement preparion is intiated by our side </p>
        </mat-step>
        <mat-step label="Document in Submission">
            <p>Agreement preparion is intiated by our side </p>
        </mat-step>
    </mat-vertical-stepper>

... and in your Typescript:

import { ViewChild, AfterViewInit } from '@angular/core';
import { MatStepper } from '@angular/material';

Component({
    .....
})
export class ComponentClass implements AfterViewInit {
    @ViewChild('stepper') stepper: MatStepper;

    ngAfterViewInit() {
        this.stepper.selectedIndex = 1; 
    }
}

Link to StackBlitz demo.