Tool – Ænima

Bass player magazine May 2001 "When I joined TooL, the band already had a few songs written, and I wanted to get Paul's sound and style-I loved it. WHen I auditioned, my approach fit what they were already doing. My MusicMan sounded good in rehearsal, but when we started recording AEnima, the StingRay didn't really work. The Music Man has a lot of lows, but some mids were missing. A friend recommended Wal basses. I tried one out and it was great. "

He used this bass in an "Aenima" instructional video for Bassiste magazine.

In this wall of basses presumably owned by Justin, a Wal MKI can be seen among them. You can tell it’s a MKI due to it having 21 frets and less upper fret access. Justin also borrowed Greg Edwards’ MKI to record the album Aenima

Jones is also a glutten for effects. On the intro to “Reflection” and “The Grudge,” both from Lateralus, he employs a vintage Moog Taurus bass pedal system. But aside from the Heil Talk Box on 10,000 Days, run through a Roland JC-120 and juiced up by a dynamic compressor, Jones’ choices of effects is less esoteric. His wah-wah pedal is a dependable Cry Baby, and his stable of other sound generators includes Boss DD3 and DD5 digital delays, a BF-2 flanger, a Line 6 Delay modeler (which also samples on the fly), a Strobostomp tuner, a tremolo pedal, chorus, and an array of distortion boxes. During experimental phases, Jones has taken the stage with multiple pedal boards at his feet. The irony of this rundown is that Jones has gone on record saying he doesn’t like to use pedals.

At 2:19, a closeup of Adam's pedalboard shows a Boss DD3 delay pedal.

2:13 on this YouTube video for DunlopTV, featuring Adam Jones's tech, Chris Leahey showing that part of Adam's distorted tone, seen in the pan of his board comes from one of the pedals that includes the Boss BF-2.