If by "align the data" you mean you want both data1 values and data2 values at some common time values, then you will probably need to interpolate both vectors onto a time vector of your choosing. This could be a little tricky given that the first 1000 values of time(:,1) and time(:,2) are pretty much constant but not equal, but anyway, in general you want to do something like this:
N = 2000;
t = linspace(min(time(:)),max(time(:)),N); % make a vector of times
data1 = interp1(time(:,1),data(:,1),t); % interpolate first column of data onto t
data2 = interp1(time(:,2),data(:,2),t); % interpolate second column of data onto t
plot(t,data1)
hold on
plot(t,data2)
Now you have both data1 and data2 with N points, at the time values given in t. You can be fancier about how you make t, such as using intersect or union.
[If by "align" you just mean see them aligned on the plot, then just do what Orion suggested.]
