HELP my puffer almost killed my new puffer
 

I have a green spotted puffer, I've had of for 3 years and I recently added a blue spot puffer that was about half its size, they were getting on fine and swimming with each other for 3 days but today I've came and looked at the tank and my new puffer is nearly dead, its top pelvic fin has been completely bitten off, half its tail is gone and it has had two chunks taken out near its eyes and a hole bitten on its back tail. What should I do? (sorry for the bad grammar it's 5am and I'm exhausted) the new puffer can still swim but appears disoriented

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Sorry to hear that. You will need to separate them to a different tank or put a partition in the tank. No other options. GL

The blue spot sadly passed away this morning. I used a net to seperate them, I believe my green spot was afraid of the blue spot causing it to attack.

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Green Spotted Puffer (Dichotomyctere nigroviridis) are known to be aggressive against other fish, sometimes completely out of the blue, but most of the time if another fish shows a weakness.
In your case, because - if I understand this correctly - you kept him alone for several years, the green spotted puffer likely perceived the new puffer as an intruder into his territory. He may have not shown aggression instantly because out of curiosity, but ultimately he just saw the new fish as competition.

BTW, how large is the tank?

He was not alone for several years. He was in with another puffer which recently passed away until last month.

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What species was that other puffer?

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