Everybody forgot about Negi, except Chisame and Asuna. Since Negi was dead, there was no Chao, and the festival went without any problem. At the end of the festival, Chisame is walking near the World Tree and wishes for another chance. The tree lights up and the Thousand Master appears to give her an opportunity to fix everything... not before Asuna WTFPWNs him for being such a terrible father. Then, Chisame awakes in the train, a normal school day, until she realizes that this is the day when Negi arrived to Mahora.
tl;dr, Negimaru is a precuel of Negima