This may or may not work but what I did once when I knew I had a leak on top of a slide on a previous RV.
Go get some "Duck" (not duct) Waterproofing tape at Walmart for around $7.50 CLICK HERE
...I believe it's a Walmart exclusive. ScotchBlue Painter's tape could also be used if "Duck" Waterproofing tape can't be found as it is waterproof but not quite as effective as "Duck" Waterproofing tape or even normal duct tape could be used in a pinch.
Shine a flashlight under the topper to see where the water is pooling on the roof of the slide. This is probably where the leak is occurring at the seam under the pool of water. The pool of water will probably be at the front or rear edges of the slide unless you see a pool of water in the middle of the slide roof that is caused by a leak leak in the topper itself. Clear off the water as best you can and get it as dry as possible. Tape over the seam of the slide's roof where the pool was.
This is, of course, ONLY a temporary fix or literally a band aid to stop the water from coming inside and may or MAY NOT work until you can get home (or to a repair facility) to diagnose exactly where the leak is originating and make a permanent repair.
Or yes, you can pull in the slide until is stops raining. Make sure there is no pooling of water anywhere under the topper before retracting the slide or you may get even more water inside.