All four issues in the set feature "virgin" variant cover versions of each issues respective A Covers (just the artwork, with no logos). Additionally, an extra copy of issue 1 featuring an exclusive "sketch" variant cover is included (a blank cover with only the logos; such covers are created so professional artists can draw custom sketches on the cover during convention appearances).
The box set's front cover is the A cover of issue 4, while the back cover is the A cover of issue 1.
At least two alternate versions of the box cover have been advertised online. On the IDW Shop, the cover is that of issue 1 cover A. On certain other online retailers, the whole wraparound is shown where the back cover is shown to be a previously unseen image of Green Hill Zone.