I've been in an Animated kick as of late. Here be crackish bunnies.
[Animated - spoilers for Season 3 and All-Spark Almanac II/ Season 4 ideas]
Don't mess with Daddy Megatron
After he became Magnus, Sentinal had heard that his new rank would allow him to use the All-Spark in special ways, but it would be a disaster to use it to destroy Megatron for good. Using this new info, Sentinal Magnus decided to visit the defeated Decepticon leader and wish that Megatron would be as weak and helpless as he was once as a sparkling.
Unfortunately, since he didn't bother to find out how to properly wield the All-Spark with his new rank (and that it didn't have all the shards), Sentinal's attempt caused a flash of light and sparkling version of Megatron appeared before them. It has almost the exact readings of Megatron's spark signature, even though very young and weak.
Realizing that this is the young version of himself and that it's possible that anything that happens to the little one could happen to him too, Megatron snatched the sparkling and used the confusion of the new Magnus to his advantage to escape. He also freed Lugnut and Blitzwing and they fled.
But things soon turn against the Decepticons. Thanks to paternal programming that suddenly got activated from looking after little Megatron, Megatron became extremely protective of his younger self. He won't even allow Lugnut, the one 'con he knew wouldn't even dare hurt the sparkling, look or even hold him. He's even more deadly and ruthless when any Autobot dared to look his way.
[Animated - Spoilers for Season 3]
Since there doesn't seem to be any other explanation; Sari started to ponder whether her other father is Megatron. Did Professor Sumdac's tinkering with the Emperor of Destruction's head somehow caused him to create a protoform somehow?