Tricky fight for Ninja. Kunoichi has a far easier time, since her Crouch P spam destroys Jubei up-close... and Kamaitachi also has a far easier time, because he's the shamefur EZMODO pick.

As usual with TNWA bosses, the crowd is a major threat; Jubei's also a fairly evasive target. Keep the former under control with throws, or launch combos off of them, at Jubei himself; ignoring them to chase him down won't end well.
Here's an okay example, on Hard difficulty. Not the fastest, but defends well against Jubei and his crowd.
And here's
a fairly shitty one, going for a faster clear time. I get beat up by the crowd, because as said, Jubei's a slippery fucker - but it's worth a look for contingency ideas.
NB the walk-up grab that starts the second fight, opposite the first's failed Shoulder Ram. While the walk-up relies on his pre-fight delay, you can execute them with confidence even
in the heat of battle, against most bosses and enemies - though you always risk getting countered (typically counter-grabbed, here). It's an abstract kinda feel.

NB Golems (the heavy loader bots) become extremely dangerous to walk
in on, once they've lost their heads. They're also invincible to Should Rams. Use Hover Dive [jump, then down+ATK] to close distance for the grab, instead.
Jubei himself isn't all that dangerous, head-to-head. Stand P spam will safely check his advance. As a general rule with Ninja, avoid Crouch P. Standing, you can absorb three jabs before knockdown; on defense, you can quickly guard and escape. On offense, tank through the first two jabs and get your iron fist around their throat. Or, as a compromise, Guard and then Tumble past their attack, grabbing on recovery. This is a particularly good counter for knockdown blows, which will floor even standing characters. (jump during Guard = tumble; 100% front-invincible, just like Kunochi's equivalent somersault)
Works exactly the same in Once Again. I guess it's more of a single-arm handspring.
While you're crouching, the slightest touch will floor you, draining anything but a max meter. Even worse, Ninja's a big target; a lot of things that'll sail over Kunoichi's head will smack him
in the face. You're also faster to bust out the vitally important Nunchaku, while standing.
All this said, grabs are probably the most effective damage dealer on Jubei, since (as seen
in the first replay's opening) he tends to teleport out of hitstun. Shoulder Ram started from just inside range will usually catch him, for an easy Atomic Drop.
If he darts
in, just punch him. Ninja's Stand P has massive range and priority, and leads quickly into Nunchaku - which won't do much damage individually, but will reset your surroundings with a quick i-framed area knockdown.
Flying kick can be ducked, and his fire pillars are more of a crowd threat... if you're caught up
in the latter, try grabbing the nearest enemy and i-framing via Giant Swing (up+ATK).
If you get caught
in his 3-hit knockdown combo, go to guard immediately. Just hold ATK during hitstun; you'll be
in guard from the next frame. It's a good idea to keep ATK depressed, when engaging enemies;
as shown here, you never know when Guard will come
in handy.
Beware of the run-
in grab he likes to use on nearby retreating players; again, if he's
in punching range, just sock him.