Day 1 Walkthru:
Follow the script and fight your tutorial battle
Next day, get out of school and head to coffee shop, then use the broken toilet on upper right.
After talking to your Secretary, head to room on the left and talk to guy in lab coat.
Then visit your room in the middle (behind the big red curtain) and get into your Halloween costume.
Go back and talk to your Secretary again for more tutorial...
Battle - This allows you to pick up missions, you can also get it from the green telephone on the surface. Note that this cost stamina.
Personnel - Assign people to task (# of people you have currently assigned is the middle # at the top). To check how many people you have to assign, just check in main menu (press X) and check the # in lower left (yup, where it is normally showing $$$ for other games).
Research - Use this to make things (instant completion as long as you have the mats)
Re-model - Re-model lv10 minions to something better. Requires 10 material alpha.
Anyway, select the only mission available.
Go talk to nurse (1map west), Then head to western-most map to loot an alpha material in the back, and also do the barrel puzzle in the middle for the secret plans.
When ready, head outside.
Paper boxes are treasure chest (they reset when you enter/exit buildings). So this is a cheap way (stamina wise) to pick up Material Alpha (can save scum to get what you want). You also want to pick up some Aphrodisiac (heart item) to get the H event going.
Store near NE corner of town map (just below your own apartment): Can pick up a cherry from the store behind me (once per day), which can be used to restore stamina (allow you to take more action).
When ready, head SW from here to reach mission 1.
Mission 1:
Make a clean save first. Clicking on this box will start your first mission (train station entrance is to the right).
After the dialogue, it will spawn a large group of people. Your goal is to get in front of these people (they will disappear). Try to get in front of as many as you can.
When you complete, the mission, save and then take the train while you are here. Reload if you did not get the train H. Unlocking the train H series cost 30 stamina each time (use the cherry you got earlier to restore 10 stamina)
Then head back to your secretary so you can assign these new personnel. I recommend infirmary (last option) to get minion H event going. You need to be 11+ lust (simply use 2 Aphrodisiac that you can get from paper boxes).
But don't start the H event yet since that will end the day. Pick up the 2nd of 3 new repeatable quests so you can recruit some more people. For this quest, we need to fight those red hair guys in town. But first, we need to talk to quest giver...
Talk to the red minion on your way out to bring 2 minions to assist you. A (attack) & C (heal) would do nicely. B is tank.
For all quests, check to make sure you talk to quest giver before starting. Some quest also have specific clothing requirement.
When you have 10 stamina left, go back to base and talk to the nurse. Select first option (assuming you raised it to 11), then go one map rest and enter the room to the right. Talk to the guy in the waiting room to proceed.
That's it for a typical day

It follows the routine so you can H/do mission while your stamina last.
When you are strong enough, the lv10 quest appears and is the first boss (GOR). Just go to the park southern most area of map. Have fun

1st quest requires you to pick up sparkle from the ground.
3rd quest requires you to talk to a minion in the base, then back to town to look for an animal.