The butterfly has always worried him. He's seen its kind before, not ink in human skin but living, dancing in the sky. They called them Chaos Butterflies and they were omens. Once, long ago, one fluttered down from silver leaves, landed on a woman he has almost forgotten, and that was when he asked her to be his wife.
People did such silly things for those butterflies.
He wonders what a Gallifreyan butterfly is doing on the arm of a simple human woman. He wonders how much chance would have to cheat to bring her to the last of the Time Lords, the only person who would know it for what it is.
Most likely it's coincidence. Random. There are only so many things a butterfly can look like, after all. He refuses to believe in destiny and fate, and knows that to a rational mind the most probable cause is chance. It is chance that Martha Jones, aged nineteen, chose to have that marked on her skin. It is chance that aged twenty-three she went to the moon and met a Time Lord. It isn't chance, not really, that he took her with him.
There were butterflies on Skaro, before the wars and the mutations. Nothing flew in that sky by the time the Doctor destroyed a world and thought the battles over. But he knows that in some versions of the myth, the Oncoming Storm can be stopped by a butterfly beating its wings at the right time. Something terrible, stopped only by a creature that no longer existed.
On Earth, the butterfly is that which summons the storm. When Martha beats her wings the Doctor tries to hold the storm in, knowing what he is capable of and terrified that Skaro was right and there will be nothing to stop him if she dies.
Of course there will be other butterflies, just as there were others before her. Some couldn't control what they summoned, were consumed by it. Some of them became storms themselves, and some ran as fast as they could to avoid that fate. The Lonely God has nothing, by his nature: the Oncoming Storm has his butterflies, for better or for worse.
He worries that this particular butterfly was chosen, shaped by the universe to control a force of nature. He worries that she wasn't, that one day he will let the storm out and Martha will not be enough to calm it. He worries that the storm might kill her.
Were it not for the ink on her arm he could pretend that she was meant for the Lonely God, who is always in company but always alone. A handmaid, a consort, an acolyte for something so much less terrible. The ink makes him think, makes him wonder and worry. He knows how easily he could rip the wings from her, tear her to pieces on a whim. He thinks of this when he feels the storm building, lets the beating of her wings whittle it to nothing. He worries that one day she will not be strong enough.
He worries that he has started to believe his own myths.