The World Is Not Enough ends with Bond killing Elektra King and Renard, which stops their plan to melt down a nuclear reactor on a submarine in Istanbul. The ending only makes sense once you see what Elektra wanted from the meltdown.
The meltdown would block rival pipelines and make her own pipeline far more valuable, so the plot was a business move dressed as terrorism. That is why the film spends its middle act in Azerbaijan, at the pipeline, and in Central Asia, where Renard takes plutonium from a decommissioned Kazakh facility: every stop feeds the final scheme. Bond kills Elektra first, then fights Renard inside the flooding submarine and kills him. With both of them dead, the plan collapses and the reactor is destroyed as Bond and Christmas Jones get clear.
The closing scene is deliberately light. Bond and Christmas celebrate the new year together in Istanbul while MI6 watches on a satellite feed, and R brushes the picture off as a technical glitch. John Cleese's R is introduced as Q's assistant, so the gag also points at the handover from Desmond Llewelyn's Q. Llewelyn made 17 appearances in the role, and this was the last, according to CBS News, which reported his death in a car crash on December 19, 1999, a few weeks after the film opened. On a second viewing, that exchange reads differently.
The film also closes on a remix of the Bond theme rather than a new end song, so the Garbage title song is heard only in its usual place over the main titles.
Opinion: the ending lands harder than the explosion because Bond has to kill a woman he was sent to protect, which makes it more personal than the finish of the earlier tomorrow never dies. The structure also mirrors the opening: the film begins with a bomb that kills a man inside MI6 headquarters and a Thames boat chase ending at the Millennium Dome, a sequence Variety's Michael Apted obituary singles out, and it ends with a threat that stays hidden until Bond reaches the submarine. Compared with the next film, die another day, the villains here are tied to one family history, the King kidnapping, rather than to a stand-alone scheme.
It is also the last film Desmond Llewelyn made as Q, a fact that gives the cast list a quiet weight on a second viewing.