Some ways to get deeper tones :
1. Swap strings (tapewounds or flats that aren't chromes)
2. Swap tone capacitors (0.1 uf is that classic deep roll-off used with some vintage P-basses)
3. Get a Mudbucker bass (EB-3, SG bass, Telecaster Bass with Neck Humbucker, etc.)
4. Change your wiring harness (if you have a passive bass)
#1, #2, #4 will work if you already have a passive bass. I'd recommend a P or PJ, or the Mudbucker one like I mentioned in #3 if you don't have one. Active basses always seem to keep the more modern, trebly/hifi sound that isn't suited for the deep dark stuff IMHO. But then again I've not tried them all. A filter-base preamp might make all the difference as I've never tried a bass with one of those in it.
The way I've got a deep-dark tone in the past was basically by either :
1. Use flatwounds on a P-bass, adjust tone accordingly
2. Get a varitone
The varitone can be set up to have some pretty deep treble cuts, but it doesn't have to sacrifice having some lighter or more subtle treble cuts. The main difference though is a varitone used like a treble cut doesn't behave the same way as a tone pot. A tone pot is more like a volume for your highs, you roll down the Db level with a set cut-off frequency. Varitone treble cuts change your cut-off frequency, but keep the Db roll-off the same (generally).
I have a varitone setup with a "deep scoop" which is kind of nice. It keeps some extreme presence-level high-end frequencies, but cuts out pretty much all the mids and some of the lower-treble. It sounds a lot like a mudbucker even though the deep-scoop is applied to a P-bass pickup.
Kellingsound on Ebay can make you a custom varitone harness that will do exactly what you want, just mention what you want and the kind of bass you have. He can also make something that has a push/pull tone pot that when pulled up makes your deep/dark tones, but when pushed down behaves like a normal tone pot. Just think of what you want and ask, he can do it for somewhere around 40-60 bucks a pop. (I have no affiliation).