I can't evaluate your code on my machine (don't have the necessary data), but are you looking for AxesOrigin?
Labeled[Show[
Plot[in, {r, 0, a},
Ticks -> {{{a, "a"}, {3 a, "3a"}, {5 a, "5a"}, {7 a, "7a"}, {9 a,
"9a"}, {12 a, "12a"}}, {0, 2.2*^-11}}, PlotRange -> All],
Plot[out, {r, a, 12 a}], PlotRange -> All, AxesStyle -> Black,
AxesLabel -> {r, "Intensity"}, LabelStyle -> Directive[Bold, Medium],
AxesOrigin -> {0, 0}
], Style["HE11", Bold, Large]]
