Each shadowrun has a Room deck, and a Trouble deck. Shuffle the room deck; cards are drawn from the top, so you can see the description before you go in. Rooms are placed adjacently. Write the room on the board; the card stays to the side.
The grid is a rough outline of the rooms in the building. The Trouble counter tracks how bad the trouble currently is. Each time Trouble is triggered, it goes up, to the maximum for the location.
There are three "clocks". The Alert clock tracks how close the location is to being on full alert, the Search clock tracks how close the players are to finding the piece of the amulet, and the Kali clock tracks whether Kali is aware of the incursion.
The players enter via a room on the edge. The first entrance is free; subsequent entrances tick the Alert clock up by one.
Rooms come from the top of the Room Deck. You can see the room description before you place a room, but it must be placed adjacent to a currently occupied room (or as an entrance). Place the room by writing the label on the room grid, and choose who is encountering the room before flipping the card. The party stays together (and is assumed to be disguised as locals), but not everyone must "encounter" any given room. Rooms must be encountered by someone before you can go beyond them, but they are only encountered once per room.
The flipped side of the Room card will have a Pass roll (with "Clear" and "Iffy" levels of success), and an Investigate roll.
Everyone who is encountering the room must make a Pass roll (most commonly stealth); people who are good may split their dice to help others, before the rolls are made. Everyone who makes a "Clear Pass" is fine. For each "Iffy Pass", the Alert clock ticks up one. If anyone fails entirely, a Trouble card is drawn. The Trouble counter ticks up after all the trouble is resolved, and it only ticks up one no matter how many cards are drawn. "T" in the Trouble cards is the current Trouble number.
After any trouble is resolved, one or more Investigate rolls are made (by the people who encountered the room). You can either make a roll or make a helper roll for someone else. People with no skill may make helper rolls for 9. If there are multiple rolls, the best is used. If "Success" is made, then the Search clock ticks forward one. If "Great Success" is made, then the Search clock ticks forward two. (If "Great Success" requires a higher difficulty, you may choose if you were trying for it after seeing your roll.)
If the Alert clock fills up, then every room automatically has one extra Trouble card drawn. If the Search clock fills up, then you have found the amulet and can leave without further incident. If the Kali clock fills up, that could be bad.
Choose what stuff you are bringing with you before starting each shadowrun. Treat this as a warning that stuff may be lost.
Everyone has a special ability to shoehorn some of your character's talents into the mechanic. Other than that, the shadowrun is basically stat + skill rolls, and not free-form. (You may be able to a shtick as a one-shot special ability, but it will cost karma.)
You may castle one item for one person, before each room.
Once per board, you may declare "I kill everyone in the room", skipping the Pass roll for everyone but ticking both the Trouble counter and Alert clock up by one.
Once per room, +2 successes to a personal "Pass" roll, or +1 success to a helper "Pass" roll.
You may declare one room per board to have kids in it after seeing the room description but before flipping it over.
You may personally avoid one Trouble entirely, and the Trouble counter does not tick up.
You may call upon Yama to clear the Kali clock, once. There may be a price later.