The Leadership Crisis (aka Deja Dude/Ultimate Ninja) was a crossover between Martin Phipps's LNH Volume 1 and wReam's Ultimate Ninja. It involved a standoff between Ultimate Ninja and Deja Dude for control of the LNH, and the resolution of the LNH traitor storyline (until it was unresolved and re-resolved later).
It can be read on the Eyrie Archive over here.
From the early chaos of the post-Cosmic Plot Device Caper LNH arose a triumvirate, leadership of the Legion shared among three – Rebel Yell, Continuity Champ, and Ultimate Ninja. But Rebel Yell left to pursue Lurking Girl, and Continuity Champ detached from humanity, leaving the Ninja as de facto leader. And not all were satisfied with this ad hoc result...
Deja Dude leads a group of underappreciated LNHers (including Procrastination Boy, Super Apathy Lad and Sidewinder) into battle against the Brotherhood of Net.Villains! When Ultimate Ninja won't believe they really managed this, some of the LNH start wondering if Deja Dude would be a better leader. Meanwhile, the LNH traitor warned of by Contraption Man is preparing to make his move, and Ultimate Ninja must find and defeat him before it's too late...
Ultimate Ninja held onto leadership by a single vote (Cliche Dude, who was angry at Deja Dude, originally known as Cliche Lad, for stealing his name). The Ninja's leadership was uncontested for a long time after that— until he had to take some time off, leading to another leadership election in a story loosely inspired by this one: the Infinite Leadership Crisis.
The long-hinted-at traitor was revealed as Myk-El, who was then killed by Ultimate Ninja. This started off a flamewar when Myk-El's creator protested. More than a year later, Dave Van Domelen resolved the issue in Constellation #27 when it was revealed that Myk-El has been corrupted by Acton Lord's influence and was not the real traitor— who, in Retcon Hour, turned out to be Contraption Man himself!