Disclaimer (it is sooo difficult right now to have a real discussion concerning Russia): Do not call me a Russian troll - you want to know what Putin thinks, so I try explain what he thinks as I see it and to provide reasons he does so. Whether they're valid or not to you is not important in this context, only whether they may be valid to Putin.
First of all, every responsible military force has pre-prepared plans for basically everything. I'm sure the Pentagon has plans for invasion of Canada and Mexico, too. If something serious occurs (like it did in Ukraine in 2014), it's too late to try and make plans which depend on thousands of little details, need to coordinate tens of thousands of actors and generally take years to formulate. It would be unreasonable to consider such plans of being of importance in any country's foreign politics.
Now to Putin's view. It is no secret that USA has spent billions of dollars in meddling with Ukrainian politics - just read this funny intercepted call between Victoria Nuland and Geoffrey Pyatt. We can call it "democracy-building", but to Russia, which has to lose a lot by losing Ukraine's cooperation, it is definitely meddling. They actually discuss who should be in the new Ukrainian government - and their man Yatsenyuk (referred to as "Yats" in the call) really got the be the Prime Minister. The same guy whom Russia suspects of fighting for the rebels in the Chechen wars. Before 2014, Ukraine was very important supplier of military hardware for Russia (for example gas turbines for russian ships and helicopters came from Ukraine), so Putin very likely sees U.S. involvement as an attempt to weaken Russia militarily. Russia is in the process of upgrading and rearming its military, and the loss of Ukrainian supplies has to be seen by Putin as a major loss for Russia and victory for its adversaries (mainly NATO). Apart from the slowing down of the rearming project, Russian Black Sea Fleet was in serious danger of losing its home port of Sevastopol, leased from Ukraine until 2042. NATO-associated Ukraine would very likely attack and scrap the agreement as unconstitutional. The resulting decrease of readiness of the Black Sea Fleet (no other Russian port comes even close to the infrastructure of Sevastopol) would be a serious blow to Russian defence of its southern flank, as in the Black Sea it borders three NATO countries - Turkey, Romania and Bulgaria, as well as the unfriendly Georgia and the Georgian breakaway region of Abkhazia, which Russia protects (also with a naval blockade if necessary). Also, is it even necessary to mention that Ukraine (and Belarus) has always been the road to invasion of Russia from Europe? To allow NATO access to Ukrainian roads, bases and airfields would be Russian capitulation on the protection of its basic security, that's just geopolitics.
So while the official Russian line is that it needs to protect the Russian nationals in Ukraine from acts of violence by Ukrainian nationalist paramilitary organizations, if you look at the previous paragraph, Putin has to see the situation as a western takeover of Ukraine. Because of the serious implications this has on Russian military readiness, he has to see it as a military conflict in stages of preparation - weakening of Russian defences. Does he seriously consider that Russia will be next? If you look at the broader picture, US withdrawal from the ABM treaty in 2001, Aegis Ashore in Romania and Poland, Russian suspicions over US involvement in the Chechnya conflict, I think he does.
he revealed the long-prepared secret plans to the Crimea takeover
Can't find this following the link you provided. Can you quote it?Mr Putin said on TV he had ordered work on "returning Crimea" to begin at an all-night meeting on 22 February. The meeting was called after Ukrainian President Viktor Yanukovych was ousted.
So, what's unclear?