Kicking back in her seat, Amaterasu starts thinking about the obvious: what kind of weakness could some hypothetical future adversary exploit to give her a virus? Sheer physical capacity wasn't a suitable vector, even a distracted future Katherine would probably have noted if it was some sort of uberplague. So it had to be some exploitable flaw. The fundamental unravelling of fusion to insert a virus that way? She was awesome, but not a reinvent-physics-to-defeat awesome. So it would have to be through some old, established weakness or technological limitation...
Say, like the loss of a limb and "improved" security from the Administration. As much as that really turned out to be worth with all the additional timeline info. Techno-organic interfaces in general would be her weakspot, since piloting the Yatagarasu to really achieve their initial design goal left so many surfaces to attack.
But maybe it was also the solution. The original design proposals called for all of this energy output to be contained within a single, intelligent container. A flawless technobiological lifeform merging the advantages of both... and in the end unable to overcome R&D's enemies: time, funding, and other technology. They could half do it, split the baselines reactor power into a mecha and push the burst fusion into her biological form. Good enough to be a war machine, even if neither of them could meet the spec, even combined. Yet that had been over a hundred years ago, the Administration had pushed the technological boundaries since then, and with all the shrapnel from this fight around, specks of future technology...
She can beat this; circumvent the future flaws by eliminating the exposed vulnerabilities; merge incompatible technologies to block the administration; complete the original research goal. She was Amaterasu, a goddess of the sun: energy seemingly without end. If her systems and the Yatagarasu's were fully merged, with all these refinements and technologies and their inbuilt energy-seeking natures it could be done. All the warnings about entropy... they were a reminder. It was her original goal: harness zero-point/vacuum energy. No doubt like any early improvement she might have trouble fully deploying that energy and spend most of it on containment, but... she already rearranged mass enough. Gravity itself might be a decent substitute for nuclear hellfire.
"Ready, little brother?"
Combining would be hard. She had some technical components, but was hardly adapted to integrate more. The Yatagarasu was able to full decompose itself for superluminal transport. Good thing that Mao had provided a working template, even if none of the inner workings were really the same technological base any more. Dissolve the Yatagarasu for transport, transfer the energy into herself rather than stopping at the boundary of flesh and from there: let instinct take over. Force of will could handle fatal injuries, this was just more of the same.
To any outside observer, all that seems to happen is the Yatagarasu dissolving into blinding light and falling inwards, drawing other debris from the battle in with it. Alarming, in the sense that any catastrophic reactor failure would be alarming, but not urgent to those assembled.
Only without the inevitable explosion, simply Amaterasu stretching, a raven on her shoulder with a noticeably metallic sheen. "I suppose you're still handling reactor subsystems, then."
"Sorry about that, I needed to address the virus problem."
After all, even if she appeared similar externally, any sort of medical scan would make it clear how different her insides had changed.
TL;DR: Absorbed mecha. Glowed a lot in doing so.