The Elite Energy is more attached to the body, spirit, and soul than the infection. It's basically fastened to them It's fixed. Since it's more connected to the body than the infection, it had more control over the body, and further more, which part of the body attacks what. This allowed the Elite Energy to force the Phoenix powers, if necessary, to attack the infection. Same thing with C2's nanites. Plus, what brings the Elite Energy, the Phoenix powers, and the nanites together is that they all have one goal: to get rid of the Plex Virus. For each body, that makes the Plex Virus outnumbered two to one.
The Elite Energy is adaptive, yes, but it can also boost the adaptivity of others. In this case, it can make the nanites and the Phoenix powers adapt more, and it did. Plus, not only does it make things adapt more, it makes them stronger. The nanites became faster, stronger, more adaptive, more powerful, and above all, better. Same goes to the Phoenix powers. Elite Energy is like the best steroid you can get.
Sure, the infection has adapted more, but the Elite Energy's adaption rate is higher. Also, the infection never experienced the Elite Energy, but neither did the Elite Energy experience the infection ever. This would make it even, but only if the two's adaption rates are the same, but they aren't. Again, the Elite Energy's adaption rate is already higher, and in fact, it adapts at an increasing rate. It can adapt at an exponential rate, and even higher, if need be.
But that's not all. The Elite Energy was destroying the Plex Virus in many different ways. One of them was by incinerating them by heat. Yes, the Virus would adapt to it, but not entirely, not for Hikaru. Hikaru's a Phoenix, so she would benefit from the heat and grow stronger. That would cause the Elite Energy to grow stronger, and thus incinerate at a much higher temperature, which would cause Hikaru to grow stronger, which caused the Elite Energy to grow stronger and incinerate and burn at a higher temperature, and it continued in a loop. This causes the Virus to struggle to keep up its adaption with the increasing heat.
For C2, the Elite Energy would convert the infection into nanites. That way, as long as the infection was there, there was plenty of resources for constructing nanites. The Elite Energy would build them very, very fast, as well. It would also make sure that the conversion was safe, and the infection was dead, but taking a bit of the infection away from the rest, and kill it before it can multiply. The process was simple and easy. Soon enough, there was more nanites than the infection in C2's body.
Another problem the infection has, is that it has to adapt to more than one thing, causing it to adapt slower to each enemy. The Elite Energy only has to adapt to one thing: the infection. The infection has to adapt to the Elite Energy and the nanites in C2's body, and the Elite Energy and the Phoenix powers in Hikaru's body. That means the Virus has to sacrifice half of its adaption to the Elite Energy and half to C2's nanites, and in Hikaru's body, it had to sacrifice half of its adaption to the Elite Energy and half to the Phoenix powers. That means it would be weaker, and would cause the adaption rate against the Elite Energy to be a lot slower. The Elite Energy, however, can commit 100% of its adaption to the infection. Therefore, it can adapt a lot quicker than the infection.
There was also magic that's defending Hikaru and C2. This was also augmented in power by the Elite Energy. This is yet another thing the infection had to worry about. It has to split its adaption into thirds for each body. This also outnumbered the Plex Virus by three to one. To make things a lot harder for the Virus, Hikaru's and C2's magic were very, very powerful. This made things a lot easier for the soul, as that was where magic was produced. The Elite Energy was doing its job in the souls, too. This resulted in easy victory for the Elite Energy in the soul. For the body, it was soon won by the Elite Energy. For the spirit, the Spirit Energy itself, another problem the Virus has to encounter, and the Elite Energy. Again, with all the problems the Plex Virus had, the Elite Energy was victorious.