Heterochromatin is composed of transposable elements (TEs) and other repeats and was once considered to be a wasteland of redundant genetic material and potentially harmful TE. Therefore, the reprogramming of heterochromatin and subsequent reactivation of TE in the immature seed and pollen is paradoxical in plants. Recent studies have shown that reactivation of TE occurs specifically in germline companion cells, the vegetative nucleus (VN) in pollen (Slotkin et al. 2009) and the endosperm in seed (Gehring et al. 2009). In the ovule, ARGONAUTE 9 (AGO9) not only has a role in silencing TE in the egg cell but also in preventing the formation of multiple asexual gametophytes (Olmedo-Monfil et al. 2010). We propose that reprogramming of heterochromatin in germline companion cells reveals TE in a controlled manner to expose them within the germline and, by the production of small interfering RNA (siRNA), ensures TE silencing in the next generation. We also propose that the mechanisms evolved to silence TE may actually promote sexual reproduction by inhibiting the formation of asexual gametes.