For this part you will need to input the correct password and "rescue" the girl, after the lengthy dialogue return to Kei's den and examine his note, after this Kei will be in the underground blue wing, after talking to Kei proceed up through the doors and run across the water into the hallway (if you enter the broken window you will find the giant blob boss but it appears to be unkillable at this point so do not go there), a cutscene will happen where Fuuno examines the red veins on the left, proceed through the rightmost door and talk to the scientist on the floor, he will instruct you to go fetch the green potion from the pharmacy room, go there and examine it and Fuuno should pick it up, return to the scientist and talk to him again, as you leave the room Fuuno should feed the potion to the red vein, now the giant blob monster has been weakened and can now be killed.
The blob will now only spawn 2 slugs now, but its acid spray attack is bugged and will poison you even if you dodge it so don't bother using an antidote as you'll just get poisoned again, the spray still deals significant damage though so dodge it anyways and try to shoot its stem and red eye when it opens, it should take about 10-15 hits before it dies.
After killing it you can return to the scientist for a lengthy backstory which mentions a virus at some point and he seems to trust you with the task to put an end to this incident, he'll also give you the key to the black double door with the autoturrets, but they're still active so go into the door past the red veins and up into the next door, if you "saved" the girl then Kei will not show up and trigger END 2 allowing you to examine the dead scientist and loot another key, the autoturrets will now not shoot you and allows you to enter the next room, there's not much to do here in the dark beside poke the console which doesn't do much, so proceed up into the darkness for the next boss.
I hope you have plenty of ammo and food/stamina for this one.
The screen will pan over to the right revealing 2 big red things which will spit out 4 purple slugs each, do not bother killing the slugs as they will just respawn, instead move in a circle to group them all together and lure the whole bunch to the left, then sprint over to the right and shoot one of the red things, after about 6-8 shots another big thing will spawn on the left, this bugger will spit out 2 (up to 5 in the end) pink blobs which will grow into jellyfish that have a rapid-firing projectile attack, so either shoot or kick the blobs before they fully mature and try to kill the left monster as soon as possible to stop the pink jellyfish from spawning, once it's dealt with you can continue shooting the red things until they're both dead.
Cue another screen panning showing a glass pane shattering and then the game kicks you back to the main menu.