As John said, "it's confusing". This is the way I understand the system. I certainly may be wrong. The rules have changed over time and may very well change again.
I think a lot of issues stem from confusion between the terms "years" and "stages" of Meaningful Use. (I don't believe CMS uses the term "phases").
The first year you participate (collect data and meet the criteria) is your year 1. That might be 2011 or 2012, if you are want to get the full incentive. (If you wait until 2013 to participate, you cannot get the full amount).
In any case, your year 1 only requires three months of data collection.
In any case, your year 1 is Stage 1 of Meaningful Use.
Your year 2 is your next year of participation.
In all cases, year 2 requires a full 12 months of data collection.
In all cases, your year 2 is Stage 1 of Meaningful Use.
Your year 3 is your third year of participation.
In all cases, this requires a full 12 months of data collection.
If you started in 2011 or 2012, you must begin to meet Stage 2 requirements in 2014, so stage 2 may begin in your 3rd or 4th year.
In 2013, we will all be using the Stage 1 rules. What you use in 2014 will be determined by when you first participated in the program. I don't think anyone gets "a year off"...unless you want to lose incentives and perhaps incur a penalty.
John, has CMS clearly stated that you will only need 3 months of attestation for Stage 2?