Before the old Soviet Union fell apart, the Crimea had long been part of Russia. For administrative simplicity, it was placed under Ukraine management. For some time, there was no real concern over who managed the Crimea, as the Russian naval base and other military assets were not under any threat.
But when the Ukraine turned towards the West, and there was a strong chance of it joining NATO, Russia's military assets there were threatened.
As the Crimea had never been "given" to the Ukraine, Putin may have seen the issue as merely asserting Russia's rightful ownership. The issue was somewhat muddied by the large number of Russian speaking peoples in Eastern Ukraine.
A look at an updated map will show that Russia limited itself to that territory which Putin considered as having belonged to USSR Russia, including that which he probably felt was needed to protected his people in Eastern Ukraine. He could have very easily taken all of the Ukraine, and what could anyone have done about it?