If you want to buy upgrades for your Seraph Bunkers, then you will need to get your hands on Warmind Bits. This is a new resource that was introduced to Destiny 2 with the Season of the Worthy. You will earn some while completing the Raising our Defences quest.
The majority of Warmind Bits that you earn will come from completing Bounties for Rasputin. You can collect Bounties from the Seraph Bunkers, should as the one located near the Sludge spawn point on the EDZ. You will get access to this while doing the Raising our Defences quest.
Rasputin will have two Weekly Bounties and four Daily Bounties. You can also get extra Bounties from him, should you wish. The Bounties will all have different objectives that you need to achieve, such as killing enemies or heading to certain locations to perform certain feats. When the Bounty is complete, you will get rewarded with Warmind Bits and experience.
Another way to get Warmind Bits is by doing the Seraph Tower Public Event in the Winding Cove, on the EDZ. This will reward you with a small amount of Warmind Bits from the chest that spawns when you finish the event. You do not need to successfully finish it to get Warmind Bits, but you will only get a small amount for failing the event.
You can also get 10 Warmind Bits each day for finishing your Daily Bunker Buster mission.
The final way we have discovered that you can get Warmind Bits is by completing Legendary Lost Sectors. Once you have enough Warmind Bits, you will be able to purchase all manner of upgrades for your Seraph Bunkers.