Loved it. The writing is gripping, the emotions intense, the journal format brilliant, and the idea original. It's even the right length, not overstaying the welcome of a situation that would surely get repetitive after a while, but instead choosing to come in a few days before the hunt of the organic by the artificial ends.
My only complain is that the ending was a bit anti-climatic. It's not a bad resolution, but having it spelled out ahead of time drained some of the impact from it. To quote How Not to Write a Novel
: "When there is a plan, things cannot go according to it. If they do, the plan becomes a spoiler." The journal entry detailing the solution should have been interrupted by the arrival of Metal Sonic just after Sonic had realized it but before he had time to explain it, and when the latter resumed writing he should just have noted what he was doing due to the hurried nature of the situation, thus keeping us in the dark about Sonic's actions until after
Metal Sonic's final log entry.
Still, definitely a great Sonic one-shot, and highly recommended.