Even though it's before Maria is killed, it still doesn't really jive.
GERALD (monitors): "If you're listening to this, then the worst has happened...
you need to know the truth. The government plans to shut
down this research facility..."
GERALD (monitors): "The government plans to cease all of our research... and
imprison all who know about you. I made a terrible mistake,
Shadow... It's all my fault... making contact with that
Comet..."
He doesn't sound too concerned that the military is coming to silence him and his beloved granddaughter. Even if imprisonment is all he's expecting, he can't possibly believe that they'd be released after serving some kind of sentence. It's effectively a death sentence. Maybe he planned to escape with Maria and abandon all his colleagues, but that's a pretty weak explanation.
When he finished Shadow is also a bit ambiguous. Either he eluded capture, found Shadow, and finished working on him before getting caught, or he was captured but allowed to continue working for the government on Prison Island and one day snuck into where they were keeping Shadow and finished him there, getting caught and executed in the process. All we have to go by is "Based on my original projections, I was able to complete my project; Shadow. I designed its mind to be perfect, pure... I will leave everything, to him." Some say he couldn've been talking about Biolizard, having somehow hidden himself in the ARK and continued his work. He definitely had to do something to Shadow though. Shadow seemed to know what the plan was, and the only way he could broadcast a video of his own death is if he made Shadow do it for him.
Edit: 'holic disabled the Guest feature! Huzzah!