The "to" in "into" means towards:
toward the inside or middle of something and about to be contained, surrounded, or enclosed by it
The only case I can think of off the top of my head to use "in to" over "into" would be in something like:
She went in to see if anyone was there.
In this case "to" means "for the purpose of doing" instead of "towards".
She went in for the purpose of seeing if anyone was there.
And, often, there could be something else between the two words and "in" would likely be replaced with "into":
She went into the house to see if anyone was there.