Start with more hides than mice
The single most protective rule in a female mouse colony is surplus shelter. Count your mice, then add hides until there is at least one more hide than mouse, and make every hide a through-route rather than a box with one door. A house with a single entrance is a trap with a roof: the mouse inside has one exit, and the mouse who wants in has one door to guard. Cardboard boxes with two holes cut in opposite walls, cork-bark tubes open at both ends, coconut shells with front and back openings, and wooden houses with a doorway on two sides all pass the test. Anything that fails it — the cute one-door cottage — comes out, whatever it cost.
Give the surplus hides different addresses. Two hides side by side count as one neighbourhood, because a dominant mouse can hold both doors at once. Spread them across the floor and up on any shelving so a mouse being pressed can put real distance and at least one wall between herself and the argument.
Build routes as loops, never dead ends
Once the hides are placed, connect them with routes that circle. Tubes from hide to hide, a bendy bridge over the middle, a rope run along the back wall: each path should let a travelling mouse keep moving forward and come out somewhere new, never nose-to-wall with a pursuer behind her. Dead ends are where cornering happens, so walk the layout with your finger before the mice go in. Every time your finger stops, the layout has a trap in it — add a tube, move a hide, or cut a second door until the loop closes.
Levels need the same treatment. A shelf reached by one ramp is a dead end with a view; add a second ramp, a hanging ladder at the far end, or a rope down to a different hide so the top floor also loops. Mice are superb climbers, so a vertical rope or knotted fabric strip is a genuine route to them, not a toy.
Food and water points that defuse tension
One food bowl in a colony is a resource worth fighting over, so abolish it. Scatter the day's food through the bedding across the whole floor and let the mice forage; a mouse cannot guard food that is everywhere. If you keep a bowl for fresh food, use two, placed at opposite ends of the enclosure with a hide or a wall of clutter between them. Fit two water bottles as well, at different heights and addresses, so nobody has to pass a rival to drink.
Then clutter the open floor on purpose. Cork pieces, short tunnels, egg boxes, toilet-roll tubes and handfuls of hay break the cage into short sight lines, and a chase that keeps losing its target usually gives up within a few inches. Open, empty floor is where pursuits build speed.
Change the layout slowly, and watch the corners
Rearrange in small steps rather than stripping and rebuilding in one afternoon, because a colony that has settled its pecking order reads a brand-new layout as new territory to argue over. Swap one hide or add one tube at a time, and keep the two-exit rule through every change. For the first evenings after any change, watch the corners of the cage at active time: repeated chasing to the same spot, a mouse sleeping alone in the open rather than in a hide, or squeaking that ends with one mouse pressed flat in a corner all tell you the loop has a gap in it. Recording the layout sketch and each mouse's favourite sleeping hide on the colony's KinsLe profile through Family Sharing means whoever in the household cleans or rebuilds the cage restores the same loops and spare hides, instead of a tidy arrangement that accidentally traps the shyest mouse.