How does Soul Eater end in the anime vs the manga?

The divergence was structural. When Bones produced the anime in 2008, the manga was mid run, so the adaptation followed Ohkubo closely through the early arcs, began adjusting with the Brew arc, and then built its own final movement: a compressed Kishin war resolved in 2009 around Maka's courage as a weapon against fear itself.

The manga had years still to run. After the anime ended, Ohkubo published the Noah arc, the rescue of Kid, the clown and madness storylines and the final war on the Moon, where the Kishin Asura's prison sits. Characters the anime barely used, including the witches' full society and the academy's eight warriors, take major roles, and Crona's story, handled ambiguously on screen, receives its full, difficult resolution.

Tone divides the endings as much as plot. The anime's finale is compact and thematic, a single idea delivered at speed. The manga's ending is cumulative: it pays off the prologues' team structure, the black blood infection from volume 3 and Maka's family story, threads a monthly series had been braiding for nine years.

Neither ending cancels the other in the market. The Bones series remains the gateway most international fans entered through, and its home video sets stand alone as a complete work; the manga is the complete story. Reading order advice follows from that: anime first for the gateway experience, or manga first for the undivided text, but expect two different wars at the end.

Ohkubo's own later work adds a footnote no 2009 viewer could have predicted: Fire Force's finale recontextualizes the Soul Eater world entirely, giving the manga's version of events a second frame that the anime, by timing alone, could never include.