There's a lot of lore (90 percent of it from Retro Studios, their efforts possibly retconned by Sakamoto), but virtually nothing in terms of meaningful character development or themes. It's a large part of why the series never really caught on in a major way -- it's sort of "empty" from a narrative standpoint. I love Metroid, though, and I'm not calling for them to try and make a grand story out of it. That's how you end up with Other M...
Other M could have been good. Metroid could certainly use some character development. The problem was that the script was awful. I'll break down Other M since mentioning it would probably cause Mama Robotnik to break out into hives. The hoops you gotta jump through to make the Prime games fit with the other games but the small amount of stuff you gotta explain to make Other M fit is too much, lol.
Samus was born and raised for the first part of her life on a Colony called K-2L. One day when Samus was only 3 years old the Space Pirates invaded the peaceful planet. The leader of the Space Pirates, Ridley, murdered her parents. The Chozo found Samus as the only survivor and took her back to Zebes to train her to fight the Space Pirates and metroids.
Some time after training with the Chozo Samus left to join the Galactic Federation marines. Samus lacked social skills due to being raised by birds and didn't get along with most people, but her commander, Adam Malcovich, was someone that she looked up to and respected. During a mission to repair a civilian ship with 300 people on board, Adam's brother Ian is sent to repair it. Something goes wrong and the drive unit Ian is working on is about to explode. Adam orders the drive unit to be detached so that the 300 civilians can be saved, sacrificing his brother in the process. Samus disagrees with this decision and leaves the marines.
Other M begins with Samus recapping the events of Super Metroid. As far as she knows she has completed the her purpose in life. Her last mission saw the complete annihilation of the metroids, the Space Pirates, and Ridley. However she does not feel as fulfilled as she should be and has doubts about the road it took to get here. A distress signal from a mysterious ship disturbs her retrospection and she flies off to investigate it.
At the mysterious ship known as the Bottle Ship, Samus encounters Adam Malcovich and his team. Samus recalls her past with Adam and regrets leaving their relationship on bad terms and eagerly wishes to repair it. Despite being much more powerful than Adam's entire team combined, she disables functions of her suit until Adam can run diagnostics on its components to determine the safety of their use around his men in a flimsy excuse to have Samus upgrade her powers that has no real impact on the story except for Samus to sarcastically ask if Adam has any objection to her activating her powers without authorization later.
Samus and Adam's investigation of the Bottle Ship uncovers a secret cloning experiment that has cloned many creatures from Zebes from a DNA sample taken from Samus' suit after Super Metroid. A mysterious figure known as the Deleter is trying to cover up what has been going on on the Bottle Ship and is destroying evidence and killing members of Adam's team. The Deleter may be a member of Adam's team and Samus becomes suspicious of everyone.
Eventually Samus encounters a revived Ridley, who she thought she had finally seen the last of since she blew up the entire planet he was on. This causes her to have PTSD episode and she freezes while Ridley attacks her. Anthony Higgs, a friend of hers, snaps her out of it, but Anthony apparently dies. Samus fights Ridley with renewed vengeance and kicks his ass, but he escapes.
Eventually Samus discovers that whoever runs the Bottle Ship has cloned metroids and she heads to the sector where they are held. Adam ambushes her and knocks her out with a deus ex machina gun as she attempts to kill a baby metroid. Adam reveals that the metroids in that sector have been made immune to ice and are thus impervious to Samus weapons. The only way to destroy them is by blowing up that whole section of the ship, but the only way to do so is from within. Adam sacrifices himself to destroy the antifreeze metroids.
Samus then uncovers the mystery of what happened on the Bottle Ship. Due to the baby metroid from Metroid II and Super Metroid forming a bond with Samus, scientists decided to create a female human android with data collected on Mother Brain called MB to control the metroids. However, they treated her like a thing, she got too powerful, and when they tried to shut her down she went HAL on their asses. MB determines that humans need to be destroyed and she set the Bottle Ship on a collision course with the Galactic Federation capital. Samus tries to stop her, but before she can the Galactic Federation storms the ship and there is a Mexican standoff. Anthony Higgs arrives and reveals that he was the one that stopped the Bottle Ship's engines and blackmails the Federation commander into allowing himself and Samus to get out of there.
Samus never finds out who the Deleter was, but players can easily figure out who it was based on evidence Samus never sees. The identity isn't important, though.
The story itself isn't bad. It's told poorly. They wrote themselves into a corner with Adam Malcovich in Metroid Fusion and there wasn't much they could do for a story set between Super Metroid and Metroid Fusion, and so not much of note occurs. The game basically exists to explain Adam in Fusion, but the way they explained Adam's sacrifice was very disappointing. Samus having more character was refreshing, but the overly lengthy and poorly written monologues as well as well as a failure to explain elements of Samus' history gave people a bad impression. Despite having a mental disorder that impairs her for a few seconds in her encounter with Ridley, she's portrayed as being more badass than ever before.
Now yes, the Prime games and Other M are incompatible because Ridley isn't given the importance to Samus he should have given their history. There's no reason you can't enjoy 2 canons. Zelda fans have 3.
