Clean up a bass track? This track was recorded so extremely saturated that some spots just blur together. Is there a way to mellow that out without redoing the entire track? It's caused by the distortion from the amp, not the settings in Sonar. I've tried getting him to run clean so I could add the FX in the mix, but the jack leg won't do it.
 
Any suggestions?

Izotope Rx3 declip, may be

You'd probably get better results by taking a stand and showing him you really can't work with this.
Whenever possible, strive to fix it at the source.

Why not record both with a Y connector. Mic and direct in on two tracks? 

I agree - anything that cleans the audio is likely going to leave it sounding pretty flat.
 
The guy needs to know that you cannot effectively alter that signal if he is applying that distortion prior to it being fed into Sonar, and that there isn't much you can do other than to redo the track properly.
 
It's really the same thing as having a guitar player add a bunch of effects ahead of his signal going into Sonar.  It may sound OK, but then you can't alter those effects through any magic in Sonar - that processed tone is what you get, because that's what he gave Sonar.
 
Good luck, 
 
Bob Bone
 

A thought - would it work to split the signal off AHEAD of where he adds the distortion, so that you feed a clean signal into Sonar, but still give him a signal that he can add distortion to for him to hear while he is playing?  (lots of direct boxes allow the signal to be split).
 
Don't know if the above would give you something that would meet the needs, but in some cases it works. That is sometimes done with guitars, to create multiple feeds into Sonar, each with a different tone, that can then be processed differently in Sonar, and blend back together to give a much richer sound than would be achieved with a single signal.
 
Bob Bone
 

I think any approach/DSP that might be able to clean up the track would still leave you wishing the recording had been done properly to begin with. While some magical FX might make the notes sound cleaner, the transients would still be suffering from the extreme compression.

I don't mind when someone wants to have "his own tone" in Sonar, and certainly I would prefer a really good guitarist to bring his own gear rather than fiddle with amp sims to create the sound that he can dial in in seconds.
However, that doesn't seem to be the case here. Without knowing more background story, I can see one of two scenarios;
1. You are paying him for recording bass on YOUR project. In which case he needs to STFU and do what you're asking, or
2. He's paying YOU to make a recording of him on HIS project. In which case you can let him listen to the recording (with the rest of the band, preferably) and say that you don't think this sound is very workable. He can either agree and redo the recording, or he won't agree and you'll deliver a crap bass sound because that's what the client wanted.

This is my suggestion:

Bottom line, you are the recording engineer. It's your job to get the sound you need, while the player is as comfortable as can be.

To do this you need certain tools. One being a direct box. That way you can get the clean sound you need and the player gets the sound he wants.

If your paying him, get your moneys worth and have him play his best. He will do this if he is confident in his playing/sound.

It's all about the "capture." As the recording engineer, you have to be ready and able to capture the feel, the sound, the moment. Whether your being paid or not.

It's hard to tell without hearing the source material however, you can try using Transient Shaper to get some definition back into the performance. A fast attack and a short decay concentrating on higher timbres could define the muddier parts a little bit.