When Zack first enters the reactor, he immediately stops to check on Tifa, who is clearly suffering from grave physical -- not to mention emotional -- wounds. He kneels at her side and she slowly awakens, asking distantly whether Shinra had really arrived with intentions to investigate the reactor. It was just an investigation, right? She had agreed to guide them because she wanted to help, and now look what happened; she hated Shinra, she hated Sephiroth, and she hated him.
Zack flinches slightly at her words, but the look of surprise is soon replaced by one of solemn resolve. He hadn't meant for this to happen, either, and he would never forgive Sephiroth or even himself. However, he wasn't going to sit by and let the bloodshed continue. He was going to put an end to it. With that he stands, leaving Tifa where she lies, and follows Sephiroth further into the reactor.
He finds the general standing before Jenova. Sephiroth speaks in a tone that is frighteningly affectionate as he coaxes his "mother" and promises her the world (quite literally), and Zack can hardly believe what he's hearing. He screams for his superior to stop, demanding to know what happened. Sephiroth leisurely turns, unfazed by the younger man's outraged cries, and explains his purpose; he is to take the Planet from the humans who have abused it and deliver it to Mother. He certainly is not about to let someone as inferior as Zack stop him, and the two quickly find themselves locked in combat.
Although he holds his own for awhile, Zack is soon overpowered and thrown clear out of the room. He crashes into one of the pods in the adjacent chamber and is knocked unconscious. Sephiroth again turns to Jenova, letting his guard down in the process.
Enter Cloud; he may be a mere guard of no name or status, but he won't stand by as his friends and family are slaughtered. In a moment of rage, he thrusts Zack's discarded weapon through Sephiroth. The general collapses, leaving Cloud to stand for a moment in shock. Finally he remembers his friends outside; throwing off his helmet, he runs to Tifa, taking her into his arms and carefully placing her out of harm's way. He puts a comforting hand on her cheek as she awakens, and the two recall their childhood promise fondly, each obviously thankful for the presence of the other in the face of everything.
When Sephiroth finally emerges with Jenova's head, Zack gasps out a request for Cloud to finish what they had begun. Resigned to his fate, Cloud once again takes up Zack's sword and charges. This time, however, Sephiroth is ready. He skewers his attacker, lifting him clear off the ground with the Masamune and throwing him to the side. Enraged by the mere human's attempts to foil his plans, Sephiroth advances again, thrusting his sword into the boy while he lies helplessly on the ground. Effortlessly, he holds him over the Mako vats far below.
In a display of true determination, Cloud firmly grabs the Masamune's blade and pulls himself back onto the platform. In no position to dump Sephiroth over the edge as was done in the original game, Cloud uses his remaining strength to throw Sephiroth away before he collapses. Sephiroth can do nothing but stare back at Cloud's glowing scowl and utter a bewildered "what are you?". Seeing that the tables have suddenly turned, the general decides to make his exit by voluntarily jumping into the Mako pools below, cradling Jenova's head with an expression of total -- not to mention frighteningly displaced -- content.
Cloud, understandably drained from the struggle, collapses on the ground, joining Tifa and Zack in a blissful state of unconsiousness. Zangan -- Tifa's martial arts master -- manages to sneak past the growing security to rescue his pupil, but the fallen SOLDIER and guard are left at the hands of the corporation, which has pulled all the stops for an all-out cover-up. Even Professor Hojo and Tseng -- the head of Shinra's science branch and elite Turks -- are present to oversee the cleanup. As Cloud is carried away on a stretcher, Hojo signals for the grunts carrying the body to stop, leaning over to inspect his new specimen, he deduces that this one must have been the one to ultimately defeat Sephiroth. More amused than moved by the remnants of the tragedy that summoned him, Hojo sends the boy away to his labs where he will spend the next five years undergoing unbearable, coma-inducing Mako treatments.
A note
Crisis Core's interpretation of the Nibelheim disaster is much closer to that of the original game's (Cloud is actually responsible for dropping Sephiroth into the Mako instead of Sephiroth voluntarily jumping in), thus rendering this version as irrelevant in the canon.
Source: Last Order
