Tokyo Ghoul Ending, Explained
The manga ends on a survival nobody expected. The anime cannot reach that ending, because it killed a character in season two that the ending depends on.
Spoilers throughout. This page assumes you have finished the series.
Which ending you get depends on what you watched, and unlike most cases of that the anime did not simply tell the story differently. It removed a piece the ending needed and then had to put it back.
The manga ending
After the Dragon crisis, Kaneki is caught in the collapse and the flooding that follows, and is pulled out by Ayato away from the reader's view. The final chapter jumps forward: Tokyo is rebuilding, ghouls and former investigators are living in the same city under an uneasy new arrangement, and Kaneki is alive, settled, and has a daughter, Ichika.
It is a much gentler close than the series earned a reputation for, which is precisely why it is argued about. A popular reading holds that none of it is real and that Kaneki was consumed by Dragon, with the epilogue as the last thing a dying mind produces. Nothing in the text requires that reading, and nothing forbids it, so it has the shape of a theory the work is content to leave standing rather than a puzzle with an answer.
Where the anime came apart
Root A, the second season, is largely anime-original, and its most consequential invention is that Hide dies during the Owl Suppression Operation.
In the manga Hide does not die there. He returns much later and is decisive in the closing stretch of the story, which means the anime disposed of a character the ending structurally depends on, two seasons before that ending.
The consequence arrives exactly as you would expect. When the adaptation reaches :re and needs him, Hide is simply alive again, with no account of how, because the source requires him and the previous season's version of events cannot be reconciled with that. The anime is not being unfaithful at that point; it is being faithful to a story it had already made itself unable to tell.
Why this keeps happening
An anime that overtakes or rewrites its source is making a bet about what the ending will need, and the bet is usually placed by people who do not know yet. Killing a supporting character early is cheap drama with a delayed invoice.
The Promised Neverland broke its ending by removing a cost, and this one broke its ending by removing a person. Compare both with Fullmetal Alchemist's 2003 series, which departed from its manga deliberately, committed to it, and built a conclusion that works on its own terms. The difference is not fidelity. It is whether anyone decided.